RetrogeneDB ID: retro_pabe_3722

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:9639474..9640196(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5
• Ensembl ID: ENSPPYG00000006169
• Aliases: None
• Description: Eukaryotic translation initiation factor 5 [Source:UniProtKB/Swiss-Prot;Acc:Q5R4L0]

Sequence

>retro_pabe_3722
GAAATTAGCCCTCCTCCACATACAGTGGAAGAAGAGGAGGATGACTGGGGGGAAGATACAACTGAGGAAGCTCAAAGGTG
CAGAACGGATGAAATCAGTGATCATGCAAAAGTTCTGATACTCCATGATGATTTGGAAAAAACAGTTGAGGAGCGGGCCA
ACATCCTGTTTGATTTTGTGAAGAAAAAGAAAGAAGAGGGTATCATTGATTTATGTGACAAAGAAATTGTTACTGAAGCA
GGACTGGATGTAAAAGCCATGGGCCCTCTTGTTCTGAATGAAGTTCTTTTTAAAGAGGAGATTAGAGAACACATAAGAAA
TACAGGCACCACTTCTTATGATTTTGTCACAACAACAAAAAAGCTCAATGGTACCTTCTTCATGGCTTTACGTGTGGGGT
AGCAATGCACCAAGCTCAGCTTATCTCTAAGATTCTAAATATCTTGAAGCAGATGTATGATGTAGATTTTTTAGAAGAAG
AGGTCGTCATCAGCTGGTCGGAAAAAAGCCTTTAAGAAACATGTCTCAAAAGAAGTTGCCAAACAGATTCGTGTCAAAGC
AGAACCATTTATAAAATGAAGGAGGCAGAGGAAGAATCTTCTGGTGGTGAAGAAGATGAAGATGAGAACATTGAGGTGGT
GTATTAGAAGACTGCCAGTGTACCTAAAGTTGAAACTGTAAAGTCCAACAACAAGGATGATGACATTGATATTGATGCCA
TT

Alignment

ORF - retro_pabe_3722 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.84 %
• Parental protein coverage: 56.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EISPPPHTMEEEEDDDWGEDTTEEAQRRRMDEISDHAKVLTLSDDLERTIEERVNILFDFVKKKKEEGVI
          EISPPPHT.EEEEDD.WGEDTTEEAQR.R.DEISDHAKVL.L.DDLE.T.EER.NILFDFVKKKKEEG.I
Retrocopy EISPPPHTVEEEEDD-WGEDTTEEAQRCRTDEISDHAKVLILHDDLEKTVEERANILFDFVKKKKEEGII

Parental  DSSDKEIVAEAERLDVKAMGPLVLTEVLFNEKIREQI-KKYRRHFLRFCHNNKKAQRYLLHGLECVVAMH
          D..DKEIV.EA..LDVKAMGPLVL.EVLF.E.IRE.I.KKYR.HFL.FCHNNKKAQ.YLLHG..C.VAMH
Retrocopy DLCDKEIVTEA-GLDVKAMGPLVLNEVLFKEEIREHI<KKYRHHFL*FCHNNKKAQWYLLHGFTCGVAMH

Parental  QAQLISKIPHILKEMYDADLLEEEVIISWSE-KASKKYVSKELAKEIRVKAEPFIKWLKE-AEEESSGGE
          QAQLISKI..ILK.MYD.D.LEEEV.ISWSE.KA.KK.VSKE.AK.IRVKAEPFIK......EE.S.G..
Retrocopy QAQLISKILNILKQMYDVDFLEEEVVISWSE>KAFKKHVSKEVAKQIRVKAEPFIK*RRQ<EEESSGG--

Parental  EDDEDENIEVVYSKTASVPKVETVKSDNKDDDIDIDAI
          E.DEDENIEVVY.KTASVPKVETVKS.NKDDDIDIDAI
Retrocopy EEDEDENIEVVY*KTASVPKVETVKSNNKDDDIDIDAI

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	0.00 RPM	165.49 RPM
SRP007412_cerebellum	0.00 RPM	204.41 RPM
SRP007412_heart	0.00 RPM	80.56 RPM
SRP007412_kidney	0.03 RPM	145.41 RPM
SRP007412_liver	0.00 RPM	164.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3722 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3722 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4782
Pan troglodytes	retro_ptro_3183

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001236	1 retrocopy	retro_cpor_577,
Homo sapiens	ENSG00000100664	1 retrocopy	retro_hsap_4782,
Monodelphis domestica	ENSMODG00000013424	1 retrocopy	retro_mdom_2000,
Nomascus leucogenys	ENSNLEG00000016105	1 retrocopy	retro_nleu_1102,
Pongo abelii	ENSPPYG00000006169	1 retrocopy	retro_pabe_3722 ,
Pan troglodytes	ENSPTRG00000006753	1 retrocopy	retro_ptro_3183,
Rattus norvegicus	ENSRNOG00000010218	2 retrocopies	retro_rnor_1781, retro_rnor_2459,