RetrogeneDB ID: retro_pabe_3530

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:4027042..4027387(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000003223
• Aliases: None
• Description: None

Sequence

>retro_pabe_3530
ATGAAGACCTTTCATGGGTTAAATGGATTCTTTCTTCTCTGTTTCTTGATATGGACCTGTGCTGGGGATTGGTCAGCTGT
TCAAGTGCAATGCACTCAGTTTTGTTTCTGTGCCAGGATTAAACCTACGATATTTCACATTTCATATACAAACCCCGATG
AAGTGTTTCTAGGAGATGGCTGCCCCATAATCTAAGTTTTGCCAAATGTTTACTATGAGTTTCACCATCATCCTGTTAAA
TGTGGTATTGTAACTAAAACTCTTCAGGAAATTCTGCTTAAAACTAATATCACGTATATCTCAAGAAACTCTTCCTGATT
TGAAATGCCTCTGTCATGTGTTGTC

Alignment

ORF - retro_pabe_3530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKTVLGFKGLFYLHSLIWTCAGDWSAIQVHCTQFWFFARIKPTIFYNLYVNPDEVFLGDGCCVTHVLPNV
          MKT..G..G.F.L..LIWTCAGDWSA.QV.CTQF.F.ARIKPTIF...Y.NPDEVFLGDGC....VLPNV
Retrocopy MKTFHGLNGFFLLCFLIWTCAGDWSAVQVQCTQFCFCARIKPTIFHISYTNPDEVFLGDGCPII*VLPNV

Parental  YYEFFYHPHDCGIVTQPLQEVLLLKTKIKHISRDSTVRSEMPLSCVV
          YYEF..HP..CGIVT..LQE..LLKT.I..ISR.S....EMPLSCVV
Retrocopy YYEFHHHPVKCGIVTKTLQEI-LLKTNITYISRNSS-*FEMPLSCVV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.72 RPM	0.17 RPM
SRP007412_cerebellum	3.04 RPM	0.00 RPM
SRP007412_heart	0.51 RPM	0.00 RPM
SRP007412_kidney	0.99 RPM	0.00 RPM
SRP007412_liver	0.70 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3530 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3530 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027348	1 retrocopy	retro_btau_1647,
Homo sapiens	ENSG00000214788	2 retrocopies	retro_hsap_373, retro_hsap_4328,
Gorilla gorilla	ENSGGOG00000016792	6 retrocopies	retro_ggor_1709, retro_ggor_2172, retro_ggor_3079, retro_ggor_3085, retro_ggor_3086, retro_ggor_383,
Nomascus leucogenys	ENSNLEG00000013194	3 retrocopies	retro_nleu_2825, retro_nleu_2997, retro_nleu_3033,
Pongo abelii	ENSPPYG00000003223	20 retrocopies	retro_pabe_1419, retro_pabe_1525, retro_pabe_1707, retro_pabe_1713, retro_pabe_1716, retro_pabe_1720, retro_pabe_1745, retro_pabe_1749, retro_pabe_1761, retro_pabe_2101, retro_pabe_3226, retro_pabe_3227, retro_pabe_3229, retro_pabe_331, retro_pabe_3530 , retro_pabe_3539, retro_pabe_3546, retro_pabe_3561, retro_pabe_3580, retro_pabe_3585,
Pan troglodytes	ENSPTRG00000034506	18 retrocopies	retro_ptro_1635, retro_ptro_2588, retro_ptro_2591, retro_ptro_2593, retro_ptro_292, retro_ptro_3066, retro_ptro_3081, retro_ptro_3082, retro_ptro_3084, retro_ptro_3085, retro_ptro_3087, retro_ptro_3088, retro_ptro_3284, retro_ptro_3289, retro_ptro_3293, retro_ptro_3300, retro_ptro_3305, retro_ptro_3309,