RetrogeneDB ID: retro_pabe_3737

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:41399927..41400839(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TNIP2
• Ensembl ID: ENSPPYG00000014545
• Aliases: None
• Description: TNFAIP3 interacting protein 2 [Source:HGNC Symbol;Acc:19118]

Sequence

>retro_pabe_3737
GAAATTGAGAGGCTTACTAAGCGACTAGAAGCGAAAGAGAGGGAGATGCAGCAGCTGCTGAGCCAGCCACAGCACGAGCG
AGAGAAGGAAGTCGTCCTGATGCGGAGGAGCATGGCGGAGGGGGAACCGGCCCGCCCCACCAGTGACGTTCTGTGCCGCT
CCTTGGCCAATGAGACCCACCAGCTGCGGAGGACGCTGACCTCCACTGCCCACATGTGTCAGCATCTGGCCAAGTGTCTG
GATGAACGACAGCATGCACAAAGGAACGTGGGGGAGAGAAGTCCTGAAAGTCAGAACATACAGGTAGGGACACCTCTGTC
CAGAGTGTTACTGAGGAAGAAAATCGACTGTTAAAACAGAAGGTGACTCATGTTGAAGACCTCAATGCCAAGTGGCAGAT
ATACGATGCCAGCATGGACGAATACATGAGGGGACTCCATGCACAGCTCAGGGGGCTGCAGACCCCCCATGAGCCCGAGC
TGATGAGGAAGGAGATCTCCCGGCTCAAGAGACAGTTGGAAGAGAAAATAAACGACTGTGCAGAATTGAAGTAGAAGCTG
GCAGGTTCTAGGACGGCCCGGGATGCTGCACTGGAATGGGTGCAGATACTGGAACAGCAGATTCTCGCTTACAAGGATGA
CTTCATGTCAGAAAGGACAGATCGGGAACAGGCTCAAGGTAGGATTCAGGAACTGGAGGAAAAGGTCACCTCTTTGCTGC
ACCAGGTGTCCTGGAGACAGGATTCTCAGGAGCCAGACGGCTGCTGGATTCACGCTGGGAGCAAAACTGCCAAGTACTTG
GCCACCGATGCAGTGGAGCTTATGGTGCCTGGTGGCTGGAGGCCTGGGACTGGGTCCCACGCAGTTGGAACCCCCTGCAG
AGGGCGGGCATCCTGGCGCAACCCAGAGAGGG

Alignment

ORF - retro_pabe_3737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.06 %
• Parental protein coverage: 91.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EIERLTERLEEKEREMQQLLNQPQHEREKEVVLLRRSMAEGERARAASDVLCRSLANETHQLRRTLTATA
          EIERLT.RLE.KEREMQQLL.QPQHEREKEVVL.RRSMAEGE.AR..SDVLCRSLANETHQLRRTLT.TA
Retrocopy EIERLTKRLEAKEREMQQLLSQPQHEREKEVVLMRRSMAEGEPARPTSDVLCRSLANETHQLRRTLTSTA

Parental  HMCQHLAKCLDERQHAQRNVGERSPD-QSEHTGGHTSVQSVIEKLQEENRLLKQKVTHVEDLNAKWQRYD
          HMCQHLAKCLDERQHAQRNVGERSP...SEHTG..TSVQSV.E...EENRLLKQKVTHVEDLNAKWQ.YD
Retrocopy HMCQHLAKCLDERQHAQRNVGERSPE<KSEHTGRDTSVQSVTE---EENRLLKQKVTHVEDLNAKWQIYD

Parental  ASRDEYVRGLHAQLRGLQIPHEPELMRKEISRLNRQLEEKINDCAEVKQELAASRTARDAALERVQMLEQ
          AS.DEY.RGLHAQLRGLQ.PHEPELMRKEISRL.RQLEEKINDCAE.K..LA.SRTARDAALE.VQ.LEQ
Retrocopy ASMDEYMRGLHAQLRGLQTPHEPELMRKEISRLKRQLEEKINDCAELK*KLAGSRTARDAALEWVQILEQ

Parental  QILAYKDDFMSERADRERAQSRIQELEEKVTSLLHQVSWRQDSREPDARRIHVGSKTAKYLATDALELMV
          QILAYKDDFMSER.DRE.AQ.RIQELEEKVTSLLHQVSWRQDS.EPD...IH.GSKTAKYLATDA.ELMV
Retrocopy QILAYKDDFMSERTDREQAQGRIQELEEKVTSLLHQVSWRQDSQEPDGCWIHAGSKTAKYLATDAVELMV

Parental  PGGWRPGTGSQ-QLEPPAEGGHPGAAQRG
          PGGWRPGTGS..QLEPPAEGGHPGA.QRG
Retrocopy PGGWRPGTGSH>QLEPPAEGGHPGATQRG

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	0.17 RPM	13.93 RPM
SRP007412_cerebellum	0.00 RPM	4.13 RPM
SRP007412_heart	0.15 RPM	7.47 RPM
SRP007412_kidney	0.07 RPM	26.82 RPM
SRP007412_liver	0.09 RPM	22.19 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3737 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3737 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3737 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4809
Gorilla gorilla	retro_ggor_2994

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000168884	1 retrocopy	retro_hsap_4809,
Gorilla gorilla	ENSGGOG00000025865	1 retrocopy	retro_ggor_2994,
Nomascus leucogenys	ENSNLEG00000000191	1 retrocopy	retro_nleu_2184,
Pongo abelii	ENSPPYG00000014545	1 retrocopy	retro_pabe_3737 ,