RetrogeneDB ID: retro_pabe_3792

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:90777064..90778283(-)
• Located in intron of: ENSPPYG00000020527

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSPPYG00000007926
• Aliases: None
• Description: eukaryotic initiation factor 4A-I [Source:RefSeq peptide;Acc:NP_001126779]

Sequence

>retro_pabe_3792
ATGTCTGCGAGCCAGGATTCCGGATCCAGAGACAATGGCCCCAATGGGATGGAGCCCGAAGGCGTCATCAAGAGTAACTG
GAATGAGATTGTTGACAGCTTTGATGACATGAATCTCTCGGAGTCCCTTCTCTGTGGCATCTACGCCTATGGTTTTGAGA
AGCCCTCTGCCATCCAGCAGCAAGCCATTCTACCTTGTATCAGGGGTATGATGAATCGCTCAAGCCCAATCTGGGACTGG
GAAAACGGCCACATTTGCCATATCGATTCTGCAGCAGATTGAATTAGAATCTAAAAGCCACCCAGGCCCTTTGTCCTAGC
ACCCACTCGAGAATTGGCTCAGCAGATACAGAAAGGTGGTCATGGCACTAGTAGACTACATGGGTGCCTCCTGTCATGCC
TGTATCAGGGGCACCAATGTGCGTGCTGAGGTGCAGAAACTGCAGATGGAAGCTCCCCACATCATCGTGGGTACCCCTGG
CCGTGTGTTTGATATGCTTAACCGGAGATACCTGTCTCCCAAATACATCAAGATGTTTGTACTGGATGAAGCTGACGAAA
TGTTAAGCCGTGGATTCAAGGACCAGATCTATGACATATTCCAAAAGCTCAACAGCAACACCCAGGTAGTTTTGCTGTCA
GCTACAATGCCTTCTGATGTGCTTGAGGTGACCAAGAAGTTCATGAGGGACCCCATTCGGATTCTTGTCAAGAAAGAAGA
GTTGACCCTGGAGGGTATCCGCCAATTCTACATCCACGTGGAACGAGAGGAGTGGAAGCTGGACACACTATGTGACTTGT
ATGAAACCCTGACCATCACCCAGGCAGTCATTTTCATCAACACCCGGAGGACAGTGGACTGGCTCACCGAGAAGATGCAT
GCTCGAGATTTCACTGTCTCTGCCATGCATGGAGATATGGACCAAAAGGAACGAGACGTGATCACGAGGGAGTTTCGTTC
TGGCTCTAGCAGAGTTTTGATTACCACTGGCCTGCTGGCCAGAGGCACTGATGTGCAGCAGGTTTCTTTAGTCATCAACT
ATGACCTTCCCACCAACAGGGAAAACTATATCCACAGAATCGGTCGAGGTGGACGGTTTGGCCGTAAAGGTGTGGCTATT
AACATGGTGACAGAAGAAGACAAGAGGACTCTTCGAGACATTGAGACCTTCTACAACACCTCCATTGAGGAAATGCCCCT
CAATGTTGCTGACCTCATC

Alignment

ORF - retro_pabe_3792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKG-
          MSASQDS.SRDNGP.GMEPEGVI.SNWNEIVDSFDDMNLSESLL.GIYAYGFEKPSAIQQ.AILPCI.G.
Retrocopy MSASQDSGSRDNGPNGMEPEGVIKSNWNEIVDSFDDMNLSESLLCGIYAYGFEKPSAIQQQAILPCIRG<

Parental  YDV-IAQAQSGTGKTATFAISILQQIELD-LKATQAL-VLAPTRELAQQIQK-VVMALGDYMGASCHACI
          YD..IAQAQSGTGKTATFAISILQQIEL..LKATQAL.VLAPTRELAQQIQK.VVMAL.DYMGASCHACI
Retrocopy YDE<IAQAQSGTGKTATFAISILQQIELE>LKATQAL>VLAPTRELAQQIQK>VVMALVDYMGASCHACI

Parental  GGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNS
          .GTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNS
Retrocopy RGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNS

Parental  NTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQA
          NTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYI.VEREEWKLDTLCDLYETLTITQA
Retrocopy NTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYIHVEREEWKLDTLCDLYETLTITQA

Parental  VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVI
          VIFINTRR.VDWLTEKMHARDFTVSAMHGDMDQKERDVI.REFRSGSSRVLITT.LLARG.DVQQVSLVI
Retrocopy VIFINTRRTVDWLTEKMHARDFTVSAMHGDMDQKERDVITREFRSGSSRVLITTGLLARGTDVQQVSLVI

Parental  NYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
          NYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
Retrocopy NYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI

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	1.11 RPM	64.30 RPM
SRP007412_cerebellum	2.31 RPM	43.53 RPM
SRP007412_heart	1.38 RPM	66.17 RPM
SRP007412_kidney	1.86 RPM	95.73 RPM
SRP007412_liver	2.57 RPM	142.08 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3792 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3792 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3792 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4873
Homo sapiens	retro_hsap_4931
Pan troglodytes	retro_ptro_3247

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000132	1 retrocopy	retro_btau_1207,
Loxodonta africana	ENSLAFG00000001107	1 retrocopy	retro_lafr_1210,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Oryctolagus cuniculus	ENSOCUG00000010375	5 retrocopies	retro_ocun_1020, retro_ocun_1326, retro_ocun_1375, retro_ocun_475, retro_ocun_934,
Pongo abelii	ENSPPYG00000007926	7 retrocopies	retro_pabe_1090, retro_pabe_1474, retro_pabe_3759, retro_pabe_3792 , retro_pabe_548, retro_pabe_846, retro_pabe_987,
Pongo abelii	ENSPPYG00000014384	2 retrocopies	retro_pabe_596, retro_pabe_677,