RetrogeneDB ID: retro_ptro_2980

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL390238.1:16350..17712(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H11A
• Ensembl ID: ENSPTRG00000001876
• Aliases: None
• Description: zinc finger CCCH-type containing 11A [Source:HGNC Symbol;Acc:29093]

Sequence

>retro_ptro_2980
GAACCCTTGTTTAGATTGGGTCTTACTGAGAGACTGGGGAAACGAAAATTTTCGGCAGGCGCTGACAGTGATCCTCCATT
AAAGCGTAGCCTGGCACAGAGGCTAGGGAAGAAAGTTGAAGCTCCGGAAACTAACACTGACGAAACACCAAAGACAGCTC
AAGTTTCCAAGTCTCTTAAGGAGCGATTAGGCATGTCAGCTGATCCAAATAATGAGGACGCAACAGATAAAGTTAATAAA
GTTGGTGAGATCCATGTGAAGACATTAGAAGAAATGCTTCTTGAAAGAGCCAGTCAGAAACATGGGGAATCGCAAACTAA
ACTCAAGACAGAAGGACCTTCAAAAACTGATGATTCTACTTCAGGAGCAAGAAGCTCCTCCACTCTCCGTATCAAAACCT
TCTCTGAGGTCCTGGCTGAAGAAGAACATAGGCAGCAGGAAGCAGAGAGACAACAAAGCAAAAAGGATACAACTTGCATG
AAGCTGAAGACTGATAGTGAAATTAAAAAAACAGTAGTTTTGCCACCCATTGTTGCCAGCAAAGGACAATCAGAGGAGCC
TGCAGGTAAAACAAAGTCCATGCAGGAGGTGCACATGAAGACGCTGGAAGAAATTAAACTGGAGAAGGCACTGAGGGTGC
AGCAGAGCTCTGAGAGCAGCACCAGCTCCCCGTCTCAACATGAGGCCACTCCGGGGGCAAGGTTGCTGCTGCGAGTCACG
CAAAGAACATGGAGGAAAGAAGAGAAGATACTTCAGGAAGGAAATGAAGTTGATTTTCAGAGCCGTATTAGAATGGAAGC
TACAGAGGCTTCAGTTGAGACCACAGGAGTTGACATCAGTAAAATTCAAGTCAAGAGATGTGCGACCATGAGAGAGATGC
GCATGCGGAAACAGCAGGAGAGGGAAAAATCAGTCTGGACACCTCTTCGGGGAGATGTAGCCTCTTGCAATACCCGAGTG
GCAGAGAAACCAGTGCTCACTGCTGTGCCAGGAATCACATGGCACCTGACCAAGCAGCTTCCCACAAAGTCATCCCAGAA
GGTGGAGGTAGAAACCTCAGGGATTGCAGACTCATTATTGAATGTGAAATGGGCAGCACAGACCTTGGAAAAAAGGGGTG
AAGCTAAACCCAAAGTGAACGTGAAGCAATCTGTGGTTAAAGTTGTGTCATCCCCCAAATTGGCCCCAAAACGTAAGGCA
GTGGAGATGCACCTTGCTGTCACTGCCGCTGTGAAGCCACTCAGCTCCAGCAGCGTCCTACAGGAACCCCCAGCCAAAAA
GGCAGCTGTGGATGCTGTTGTCCTGCTTGTCTCTGAGGACAAATCAGTCACTGTGCCTGAAGCAGAAAATCCTAGAGACA
GT

Alignment

ORF - retro_ptro_2980 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 55.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPLVRLSLTERLGKRKFSAGGDSDPPLKRSLAQRLGKKVEAPETNIDKTPKKAQVSKSLKERLGMSADPD
          EPL.RL.LTERLGKRKFSAG.DSDPPLKRSLAQRLGKKVEAPETN.D.TPK.AQVSKSLKERLGMSADP.
Retrocopy EPLFRLGLTERLGKRKFSAGADSDPPLKRSLAQRLGKKVEAPETNTDETPKTAQVSKSLKERLGMSADPN

Parental  NEDATDKVNKVGEIHVKTLEEILLERASQKRGELQTKLKTEGPSKTDDSTSGARSSSTIRIKTFSEVLAE
          NEDATDKVNKVGEIHVKTLEE.LLERASQK.GE.QTKLKTEGPSKTDDSTSGARSSST.RIKTFSEVLAE
Retrocopy NEDATDKVNKVGEIHVKTLEEMLLERASQKHGESQTKLKTEGPSKTDDSTSGARSSSTLRIKTFSEVLAE

Parental  KKHRQQEAERQKSKKDTTCIKLKIDSEIKKTVVLPPIVASRGQSEEPAGKTKSMQEVHIKTLEEIKLEKA
          ..HRQQEAERQ.SKKDTTC.KLK.DSEIKKTVVLPPIVAS.GQSEEPAGKTKSMQEVH.KTLEEIKLEKA
Retrocopy EEHRQQEAERQQSKKDTTCMKLKTDSEIKKTVVLPPIVASKGQSEEPAGKTKSMQEVHMKTLEEIKLEKA

Parental  LRVQQSSESSTSSPSQHEATPGARRLLRITKRTGMKEEKNLQEGNEVDSQSSIRTEAKEASGETTGVDIT
          LRVQQSSESSTSSPSQHEATPGAR.LLR.T.RT..KEEK.LQEGNEVD.QS.IR.EA.EAS.ETTGVDI.
Retrocopy LRVQQSSESSTSSPSQHEATPGARLLLRVTQRTWRKEEKILQEGNEVDFQSRIRMEATEASVETTGVDIS

Parental  KIQVKRCETMREKHMQKQQEREKSVLTPLRGDVASCNTQVAEKPVLTAVPGITRHLTKRLPTKSSQKVEV
          KIQVKRC.TMRE..M.KQQEREKSV.TPLRGDVASCNT.VAEKPVLTAVPGIT.HLTK.LPTKSSQKVEV
Retrocopy KIQVKRCATMREMRMRKQQEREKSVWTPLRGDVASCNTRVAEKPVLTAVPGITWHLTKQLPTKSSQKVEV

Parental  ETSGIGDSLLNVKCAAQTLEKRGKAKPKVNVKPSVVKVVSSPKLAPKRKAVEMHAAVIAAVKPLSSSSVL
          ETSGI.DSLLNVK.AAQTLEKRG.AKPKVNVK.SVVKVVSSPKLAPKRKAVEMH.AV.AAVKPLSSSSVL
Retrocopy ETSGIADSLLNVKWAAQTLEKRGEAKPKVNVKQSVVKVVSSPKLAPKRKAVEMHLAVTAAVKPLSSSSVL

Parental  QEPPAKKAAV-AVVPLVSEDKSVTVPEAENPRDS
          QEPPAKKAAV.AVV.LVSEDKSVTVPEAENPRDS
Retrocopy QEPPAKKAAVDAVVLLVSEDKSVTVPEAENPRDS

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	80.24 RPM
SRP007412_cerebellum	0.00 RPM	108.37 RPM
SRP007412_heart	0.00 RPM	51.94 RPM
SRP007412_kidney	0.00 RPM	98.10 RPM
SRP007412_liver	0.00 RPM	55.68 RPM
SRP007412_testis	0.95 RPM	101.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2980 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2980 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000058673	2 retrocopies	retro_hsap_3481, retro_hsap_508,
Monodelphis domestica	ENSMODG00000001184	1 retrocopy	retro_mdom_1449,
Mus musculus	ENSMUSG00000026464	2 retrocopies	retro_mmus_3323, retro_mmus_564,
Otolemur garnettii	ENSOGAG00000000243	1 retrocopy	retro_ogar_3250,
Pan troglodytes	ENSPTRG00000001876	5 retrocopies	retro_ptro_2980 , retro_ptro_2981, retro_ptro_2991, retro_ptro_380, retro_ptro_382,
Rattus norvegicus	ENSRNOG00000002993	3 retrocopies	retro_rnor_1570, retro_rnor_1673, retro_rnor_602,