[Genome] Calulation of Intron phase with refGene

Philge Philip philgev2 at gmail.com
Tue Dec 19 03:02:57 PST 2006


Sir
	I am Philge Philip, research assistant from India, doing a project
related to sequence analysis. Recently as part of my project i have
calculated the intron phases of all genes in human.I have used refGene
entries to confirm whether the intron phases i calculated are
correct.I like to know what the last '0' value represent in the intron
phases in refGene entry given below.The intron phases i got in my
calculation are also given below each entry.

refGene Entry :
303	NM_005465	chr1	-	241733106	242073176	241735173	242073095	13	241733106,241742248,241775434,241782653,241793644,241802850,241843595,241845020,241867535,241875817,241894696,241925515,242073049,	241735259,241742351,241775522,241782868,241793773,241802973,241843664,241845086,241867667,241875962,241894808,241925641,242073176,	0	AKT3	cmpl	cmpl	1,0,2,0,0,0,0,0,0,2,1,1,0,

Calculated intron phase for NM_005465 by myself: 1, 0, 2, 0, 0, 0, 0,
0, 0, 2, 1, 1,?

and I like to know what the  second '0' value represent in the intron
phases in refGene entry given below.
	
refGene Entry: 1766	NM_021948	chr1	+	154878363	154895942	154882470	154895550	14	154878363,154882462,154883216,154883923,154884398,154884983,154887871,154888663,154892697,154893353,154894090,154894542,154894958,154895442,	154878691,154882561,154883591,154884098,154884526,154885277,154888105,154889308,154892805,154893512,154894173,154894687,154895149,154895942,	0	BCAN	cmpl	cmpl	-1,0,1,1,2,1,1,1,1,1,1,0,1,0,

Calculated intron phase for NM_021948 by myself: -1, ?, 1, 1, 2, 1, 1,
1, 1, 1, 1, 0, 1, 0

Please guide me to understand the intron phase representation in refGene.

Thanks
Philge Philip


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