RetrogeneDB ID: retro_ptro_25

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:113360416..113361856(+)
• Located in intron of: ENSPTRG00000017137

Retrocopy information

• Ensembl ID: ENSPTRG00000017138
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ZRSR2
• Ensembl ID: ENSPTRG00000021693
• Aliases: None
• Description: zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2 [Source:HGNC Symbol;Acc:23019]

Sequence

>retro_ptro_25
ATGGCTGCACTTGAGAAGATGACGTTTCCCAAGAAGATGACATTTCCAGAGAAACCAAGCCACAAAAAGTACAGGGCCGC
CCTGAAGAAGGAGAAACGAAAGAAACGTCGGCAGGAACTTGCTCGACTGAGAGACTCAGGACTCTCACAGGAGGAGGAAG
AGGACACTTTTATTGAAGAACAACAACTAGAAGAAGAGAAGCTATTGGAAAGAGAGAGGGAAAGATTACATGAGGAGTGG
TTGCTGAGAGAGCAGAAGGCACAAGAAGAATTCAGAATAAAGAAGGAAAAGGAAGAGGTGGCTAAAAAATGGCAAGAAGA
ACAAGAGAGAAAGTTAAAGGAACAATGGAAAGAACAGCAGAGGAAAGAGAGAGAAGAGGAGGAGCAGAAACAACAGGAGA
AGAAAGAAAAAGAGGAAGCTGTGCAGAAGATGCTGGATCAGGCTGAAAATGATTTAGAAAATGGTACCACATGGCAAAAC
CCAGAACCACCCGTGGATTTCAGAGTAATGGAGAAGGATCGAGCTAATTGTCCCTTCTACAGTAAAACAGGAGCTTGCAG
ATTTGGAGACAGATGTTCACGTAAACATAATTTCCCAACATCCAGTCCTACCCTTCTTATTAAGAGCATGTTTACAACGT
TTGGAATGGAGCAGTGCAGGAGGGATGACTATGACCCTGACGCAAGCCTGGAGTTCAGCGAGGAAGAAACCTACCAACAG
TTCCTAGATTTCTATGAGGATGTGTTGCCCGAGTTCAAGAACGTGGGGAAAGTGATTCAGTTCAAGGTCAGCTGCAATTT
GGAACCTCACCTGAGGGGCAATGTATATGTTCAGTACCAGTCGGAAGAAGAATGCCAAGCAGCCCTTTCTCTGTTTAACG
GACGATGGTATGCAGGACGACAGCTGCAATGTGAATTCTGCCCAGTGACGCGGTGGAAAATGGCGATTTGTGGTTTATTT
GAAATACAACAATGTCCAAGAGGAAAACACTGCAACTTTCTTCATGTGTTCAGAAATCCCAACAATGAATTCTGGGAAGC
TAATAGAGACATCTACTTGTCTCCAGATCAGACTGGCTCCTCCTTTGGCAAGAACTCCGAGAGGAGGGAGAAGATGGGCC
ACCACGACCACTACTACAGCAGGCAGCGGGGAAGGAGAAACCCTAGTCCAGACCACACCTACAAAAGAAATGGGGAATCC
GAGAGAAAAAAGAGTAGTCATAGGGGGAAGAAATCTCACAAACGCACATCAAAGAGTCGGGAGAGGCACAATTCACCAAG
CAGAGGAAGAAATAGGCACCGCAGCTGGGACCAGGGCCGCCGGAGCCAGAGCCGCAGGAGCCACCGCAGCCGGAGCCAAA
GTTCCTCTAGGTGCCGAAGTCGTGGCAGGAGGAGGTCGGGTAATAGAGACAGAACTGTTCAGAGTCCCAAATCCAAATAA

Alignment

ORF - retro_ptro_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPEKMTFPEKPSHKKYRAALKKEKRKKRRQELARLRDSGLSQKEEEEDTFIEEQQLEEEKLLERERQR
          M..P.KMTFPEKPSHKKYRAALKKEKRKKRRQELARLRDSGLSQ.EEEEDTFIEEQQLEEEKLLERER.R
Retrocopy MTFPKKMTFPEKPSHKKYRAALKKEKRKKRRQELARLRDSGLSQ-EEEEDTFIEEQQLEEEKLLERERER

Parental  LHEEWLLREQKAQEEFRIKKEKEEAAKKRQEEQERKLKEQWEEQQRKEREEEEQKQQEKKEKEEALQKML
          LHEEWLLREQKAQEEFRIKKEKEE.AKK.QEEQERKLKEQW.EQQRKEREEEEQKQQEKKEKEEA.QKML
Retrocopy LHEEWLLREQKAQEEFRIKKEKEEVAKKWQEEQERKLKEQWKEQQRKEREEEEQKQQEKKEKEEAVQKML

Parental  DQAENELENGTTWQNPEPPVDFRVMEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKSMFTTFG
          DQAEN.LENGTTWQNPEPPVDFRVMEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKSMFTTFG
Retrocopy DQAENDLENGTTWQNPEPPVDFRVMEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKSMFTTFG

Parental  MEQCRRDDYDPDASLEYSEEETYQQFLDFYEDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQYQSEEEC
          MEQCRRDDYDPDASLE.SEEETYQQFLDFYEDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQYQSEEEC
Retrocopy MEQCRRDDYDPDASLEFSEEETYQQFLDFYEDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQYQSEEEC

Parental  QAALSLFNGRWYAGRQLQCEFCPVTRWKMAICGLFEIQQCPRGKHCNFLHVFRNPNNEFWEANRDIYLSP
          QAALSLFNGRWYAGRQLQCEFCPVTRWKMAICGLFEIQQCPRGKHCNFLHVFRNPNNEFWEANRDIYLSP
Retrocopy QAALSLFNGRWYAGRQLQCEFCPVTRWKMAICGLFEIQQCPRGKHCNFLHVFRNPNNEFWEANRDIYLSP

Parental  DRTGSSFGKNSERRERMGHHDDYYSRLRGRRNPSPDHSYKRNGESERKRSSHRGKKSHKRTSKSRERHNS
          D.TGSSFGKNSERRE.MGHHD.YYSR.RGRRNPSPDH.YKRNGESERK.SSHRGKKSHKRTSKSRERHNS
Retrocopy DQTGSSFGKNSERREKMGHHDHYYSRQRGRRNPSPDHTYKRNGESERKKSSHRGKKSHKRTSKSRERHNS

Parental  RSRGRNRDRSRDRSRGRGSRSRSRRSRRSRSQSSSRSRSRGRRRSGNRDRTVQSPKSK
          .SRGRNR.RS.D.....G.RS.SRRS.RSRSQSSSR.RSRGRRRSGNRDRTVQSPKSK
Retrocopy PSRGRNRHRSWD----QGRRSQSRRSHRSRSQSSSRCRSRGRRRSGNRDRTVQSPKSK

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	3.74 RPM	13.85 RPM
SRP007412_cerebellum	11.90 RPM	32.26 RPM
SRP007412_heart	5.65 RPM	14.43 RPM
SRP007412_kidney	5.52 RPM	15.98 RPM
SRP007412_liver	3.80 RPM	14.44 RPM
SRP007412_testis	9.91 RPM	4.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_25 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_25 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_25 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_39

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009333	1 retrocopy	retro_fcat_44,
Homo sapiens	ENSG00000169249	1 retrocopy	retro_hsap_39,
Gorilla gorilla	ENSGGOG00000011962	1 retrocopy	retro_ggor_1422,
Macaca mulatta	ENSMMUG00000014054	1 retrocopy	retro_mmul_2030,
Mus musculus	ENSMUSG00000031370	1 retrocopy	retro_mmus_233,
Nomascus leucogenys	ENSNLEG00000009496	1 retrocopy	retro_nleu_1,
Pan troglodytes	ENSPTRG00000013952	2 retrocopies	retro_ptro_1000, retro_ptro_549,
Pan troglodytes	ENSPTRG00000021693	1 retrocopy	retro_ptro_25 ,
Rattus norvegicus	ENSRNOG00000033176	1 retrocopy	retro_rnor_176,
Tarsius syrichta	ENSTSYG00000005278	1 retrocopy	retro_tsyr_1826,