RetrogeneDB ID: retro_ptro_382

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:199521873..199523432(-)
• 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_382
ATGCCTAATCAAGGAGAAGACTGCTATTTTTTTTTCTATTCTACATGTACCAAAGGTGACAGCTGCCCATTCCGTCACTG
TGAAGCTGCACTAGGAAATGAAACTGTTTGCACATTATGGCAAGAAGGGCGCTGTTTTCGACGGGTGTGCAGGTTTCGGC
ACATGGAGATTGATAAAAAACGCAGTGAAATTCCTTGTTATTGGGAAAATCAGCCAACAGGATGTCAAAAATTAAACTGC
GCTTTCCATCACAATAGAGGACGATATGTTGATGGCCTTTTCCTACCTCCGAGCAAAAGTGTGTTGCCCACTGTGCCTGA
CTCACCAGAAGAGGAAGTGAAGGCTAGCCAACTTTCAGTTCAGCAGAACAAATTGTCTGTCCAGTCCAATCCTTCCCCTC
AGCTGCGGAGCGTTATGAAAGTAGAAAGTTCCGAAAATGTTCCTAGCCCCAAGCATCCAGCAGTTGTAATTAATGCTGCA
GATGATGATGAAGATGATGATGATCAGTTTTCTGAGGAAGGTGATGAAACCAAAACACCTACCCTGCAACCAACTCCTGA
AGTTCACAATGGATTACGAGTGACTTCTGTCCGGAAACCTGCAGTCAATATAAAGCAAGGTGAATGTTTGCATTTTGGAA
TAAAAACTCTTGAGGAAATTAAGTCAAAGAAAACGAAGGAAAAATCTGAGGAGCAAGGCGAGGGTTCTTCAGGAGTTTCC
AGTCTTTTACTCCACCCTGAGCCTGTTCCAGGTCCTGAAAAAGAAAATGTCGGGACTGTGGTGAGGACAGTAACTCTCTC
CACCAAACAAGGAGAAGAACCCTTGGTTAGATTGGGTCTTACTGAGAGACTGGGGAAACGAAAATTTTCGGCAGGCGGTG
ACAGTGATCCTCCATTAAAGCGTAGCCTGGCACAGAGGCTAGGGAAGAAAGTTGAAGCTCCAGAAACTAACACTGACGAA
ACACCCAAGAAAGCTCAAGTTTCCAAGTCTCTTAAGGAGCGATTAGGCATGTCAGCTGATCCAAATAATGAGGACGCAAC
AGATAAAGTTAATAAAGTTGGTGAGATCCATGTGAAGACATTAGAAGAAATGCTTCTTGAAAGAGCCAGTCAGAAACATG
GGGAATCGCAAACTAAACTCAAGACAGAAGGACCTTCAAAAACTGATGATTCTACTTCAGGAGCAAGAAGCTCCTCCACT
ATCCGTATCAAAACCTTCTCTGAGGTCCTGGCTGAAGAAGAACATAGGCAGCAGGAAGCAGAGAGACAAAAAAGCAAAAA
GGATACAACTTGCATCAAGCTAAAGACTGATAGTGAAATTAAAAAAACAGTAGTTTTGCCACCCATTGTTGCCAGCAAAG
GACAATCAGAGGAGCCTGCAGGTAAAACAAAGTCCATGCAGGAGGTGCACATGAAGACGCTGGAAGAAATTAAACTGGAG
AAGGCACTGAGGGTGCAGCAGAGCTCTGAGAGCAGCACCAGCTCCCCGTCTCAACATGAGGCCACTCCCCAGGGCAGGTG
CTGCTGCGAATCACCGAAGAAACTGGAGGAAAAAGAGAG

Alignment

ORF - retro_ptro_382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.75 %
• Parental protein coverage: 64.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPNQGEDCYFFFYSTCTKGDSCAFRHCEAALGNETVCTLWQEGRCFRQVCRFRHMEIDKKRSEIPCYWEN
          MPNQGEDC....YSTCTKGDSC.FRHCEAALGNETVCTLWQEGRCFR.VCRFRHMEIDKKRSEIPCYWEN
Retrocopy MPNQGEDCXXXXYSTCTKGDSCPFRHCEAALGNETVCTLWQEGRCFRRVCRFRHMEIDKKRSEIPCYWEN

Parental  QPTGCQKLNCAFHHNRGRYVDGLFLPPSKTVLPTVPESPEEEVKASQLSVQQNKLSVQSNPSPQLRSVMK
          QPTGCQKLNCAFHHNRGRYVDGLFLPPSK.VLPTVP.SPEEEVKASQLSVQQNKLSVQSNPSPQLRSVMK
Retrocopy QPTGCQKLNCAFHHNRGRYVDGLFLPPSKSVLPTVPDSPEEEVKASQLSVQQNKLSVQSNPSPQLRSVMK

Parental  VESSENVPSPTHPPVVINAADDDEDDDDQFSEEGDETKTPTLQPTPEVHNGLRVTSVRKPAVNIKQGECL
          VESSENVPSP.HP.VVINAA........QFSEEGDETKTPTLQPTPEVHNGLRVTSVRKPAVNIKQGECL
Retrocopy VESSENVPSPKHPAVVINAAXXXXXXXXQFSEEGDETKTPTLQPTPEVHNGLRVTSVRKPAVNIKQGECL

Parental  NFGIKTLEEIKSKKMKEKSKKQGEGSSGVSSLLLHPEPVPGPEKENVRTVVRTVTLSTKQGEEPLVRLSL
          .FGIKTLEEIKSKK.KEKS..QGEGSSGVSSLLLHPEPVPGPEKENV.TVVRTVTLSTKQGEEPLVRL.L
Retrocopy HFGIKTLEEIKSKKTKEKSEEQGEGSSGVSSLLLHPEPVPGPEKENVGTVVRTVTLSTKQGEEPLVRLGL

Parental  TERLGKRKFSAGGDSDPPLKRSLAQRLGKKVEAPETNIDKTPKKAQVSKSLKERLGMSADPDNEDATDKV
          TERLGKRKFSAGGDSDPPLKRSLAQRLGKKVEAPETN.D.TPKKAQVSKSLKERLGMSADP.NEDATDKV
Retrocopy TERLGKRKFSAGGDSDPPLKRSLAQRLGKKVEAPETNTDETPKKAQVSKSLKERLGMSADPNNEDATDKV

Parental  NKVGEIHVKTLEEILLERASQKRGELQTKLKTEGPSKTDDSTSGARSSSTIRIKTFSEVLAEKKHRQQEA
          NKVGEIHVKTLEE.LLERASQK.GE.QTKLKTEGPSKTDDSTSGARSSSTIRIKTFSEVLAE..HRQQEA
Retrocopy NKVGEIHVKTLEEMLLERASQKHGESQTKLKTEGPSKTDDSTSGARSSSTIRIKTFSEVLAEEEHRQQEA

Parental  ERQKSKKDTTCIKLKIDSEIKKTVVLPPIVASRGQSEEPAGKTKSMQEVHIKTLEEIKLEKALRVQQSSE
          ERQKSKKDTTCIKLK.DSEIKKTVVLPPIVAS.GQSEEPAGKTKSMQEVH.KTLEEIKLEKALRVQQSSE
Retrocopy ERQKSKKDTTCIKLKTDSEIKKTVVLPPIVASKGQSEEPAGKTKSMQEVHMKTLEEIKLEKALRVQQSSE

Parental  SSTSSPSQHEATPGAR-RLLRITKRTGMKEE
          SSTSSPSQHEATP..R..LLRIT..TG.K.E
Retrocopy SSTSSPSQHEATPQGR<VLLRITEETGGKRE

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	0.13 RPM	80.24 RPM
SRP007412_cerebellum	0.04 RPM	108.37 RPM
SRP007412_heart	0.00 RPM	51.94 RPM
SRP007412_kidney	0.00 RPM	98.10 RPM
SRP007412_liver	0.07 RPM	55.68 RPM
SRP007412_testis	7.38 RPM	101.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_382 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_382 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,