RetrogeneDB ID: retro_ptro_2303

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:142050333..142051236(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000017344
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ptr-mir-621
• Ensembl ID: ENSPTRG00000005809
• Aliases: None
• Description: ptr-mir-621 [Source:miRBase;Acc:MI0008819]

Sequence

>retro_ptro_2303
ATGAAGTCCGGTCCTGGCATCCAAGCCGCCATCGACCTCACAGCGGGGGCCGCAGGGGGGACAGCGTGTGTACTGACTGG
GCAGCCCTTCGACACAATAAAAGTGAAGATGCAGACGTTCCCTGACCTGTACAAGGGCCTCACCGACTGCTTCCTGAAGA
CATACGCCCAAGTGGGTCTCCGGGGCTTCTACAAGGGCACCGGCCCGGCACTTATGGCCTACGTCGCCGAAAACTCGGTC
CTCTTCATGTGCTACGGGTTCTGCCAGCAGTTTGTCAGGAAAGTGGCTGGAATGGACAAGCAGGCAAAGCTGAGTGATCT
CCAGACTGCAGCCGCGGGGTCCTTCGCCTCTGCATTTGCTGCACTGGCTCTCTGCCCCACTGAGCTTGTGAAGTGCCGGC
TACAGACCATGTATGAAATGGAGATGTCAGGGAAGATAGCAAAAAGCCATAATACAATTTGGTCTGTCGTGAAGGGTATC
CTTAAAAAGGATGGCCCCTTGGGCTTCTACCATGGACTCTCGAGTACTCTACTTCAAGAAGTACCGGGTTACTTCTTTTT
CTTTGGTGGCTATGAACTGAGCCGATCGTTTTTTGCGTCAGGGAGATCAAAAGATGAACTAGGCCCTGTCCATTTGATGT
TAAGTGGTGGAGTTGCTGGAATTTGCCTGTGGCTTGTCGTGTTCCCAGTGGATTGTATTAAATCCAGAATTCAAGTTCTT
TCCATGTATGGGAAACAGGCAGGATTTATTGGTACCCTCTTAAGTGTTGTGAGAAATGAAGGAATAGTAGCCTTATATTC
TGGACTGAAAGCTACTATGATTCGAGCAATCCCTGCCAATGGGGCACTGTTTGTGGCCTACGAATACAGCAGGAAGATGA
TGATGAACCAGTTGGAAGCATAC

Alignment

ORF - retro_ptro_2303 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSNPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPA
          MKS.P.IQAAIDLTAGAAGGTACVLTGQPFDT.KVKMQTFPDLY.GLTDC.LKTY.QVG.RGFYKGT.PA
Retrocopy MKSGPGIQAAIDLTAGAAGGTACVLTGQPFDTIKVKMQTFPDLYKGLTDCFLKTYAQVGLRGFYKGTGPA

Parental  LIANIAENSVLFMCYGFCQQVVRKVAGLDKQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEM
          L.A..AENSVLFMCYGFCQQ.VRKVAG.DKQAKLSDLQ.AAAGSFASAFAAL.LCPTELVKCRLQTMYEM
Retrocopy LMAYVAENSVLFMCYGFCQQFVRKVAGMDKQAKLSDLQTAAAGSFASAFAALALCPTELVKCRLQTMYEM

Parental  ETSGKIAKSQNTVWSVIKSILRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPV
          E.SGKIAKS.NT.WSV.K.IL.KDGPLGFYHGLSSTLL.EVPGYFFFFGGYELSRSFFASGRSKDELGPV
Retrocopy EMSGKIAKSHNTIWSVVKGILKKDGPLGFYHGLSSTLLQEVPGYFFFFGGYELSRSFFASGRSKDELGPV

Parental  PLMLSGGVGGICLWLAVYPVDCIKSRIQVLSMSGKQAGFIRTFISVVKDEGITALYSGLKPTMIRAFPAN
          .LMLSGGV.GICLWL.V.PVDCIKSRIQVLSM.GKQAGFI.T..SVV..EGI.ALYSGLK.TMIRA.PAN
Retrocopy HLMLSGGVAGICLWLVVFPVDCIKSRIQVLSMYGKQAGFIGTLLSVVRNEGIVALYSGLKATMIRAIPAN

Parental  GALFLAYEYSRKLMMNQLEAY
          GALF.AYEYSRK.MMNQLEAY
Retrocopy GALFVAYEYSRKMMMNQLEAY

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	0.07 RPM	4.43 RPM
SRP007412_cerebellum	0.07 RPM	3.84 RPM
SRP007412_heart	0.03 RPM	3.38 RPM
SRP007412_kidney	0.03 RPM	9.62 RPM
SRP007412_liver	0.10 RPM	52.64 RPM
SRP007412_testis	24.13 RPM	26.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2303 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2303 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2303 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_44
Gorilla gorilla	retro_ggor_2294
Pongo abelii	retro_pabe_82

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017797	1 retrocopy	retro_cjac_1776,
Cavia porcellus	ENSCPOG00000005570	2 retrocopies	retro_cpor_105, retro_cpor_107,
Equus caballus	ENSECAG00000007666	1 retrocopy	retro_ecab_72,
Homo sapiens	ENSG00000102743	1 retrocopy	retro_hsap_44,
Gorilla gorilla	ENSGGOG00000025261	1 retrocopy	retro_ggor_2294,
Microcebus murinus	ENSMICG00000007218	1 retrocopy	retro_mmur_18,
Macaca mulatta	ENSMMUG00000022585	1 retrocopy	retro_mmul_199,
Nomascus leucogenys	ENSNLEG00000001185	1 retrocopy	retro_nleu_1704,
Otolemur garnettii	ENSOGAG00000009380	1 retrocopy	retro_ogar_490,
Pongo abelii	ENSPPYG00000005307	1 retrocopy	retro_pabe_82,
Pan troglodytes	ENSPTRG00000005809	1 retrocopy	retro_ptro_2303 ,
Pteropus vampyrus	ENSPVAG00000010393	1 retrocopy	retro_pvam_15,
Ictidomys tridecemlineatus	ENSSTOG00000007840	1 retrocopy	retro_itri_726,
Tupaia belangeri	ENSTBEG00000017239	1 retrocopy	retro_tbel_4583,