RetrogeneDB ID: retro_ptro_380

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:198806566..198807844(-)
• 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_380
CCTTCAAAAACTGATGATTCTACTTCAGGAGCAAGAAGCTCCTCCACTATCCGTATCAAAACCTTCTCTGAGGTCCTGGC
TGAAGAAGAACATAGGCAGCAGGAAGCAGAGAGACAAAAAAGCAAAAAGGATACAACTTGCATCAAGCTAAAGACTGATA
GTGAAATTAAAAAAACAGTAGTTTTGCCACCCATTGTTGCCAGCAAAGGACAATCAGAGGAGCCTGCAGGTAAAACAAAG
TCCATGCAGGAGGTGCACATGAAGACGCTGGAAGAAATTAAACTGGAGAAGGCACTGAGGGTGCAGCAGAGCTCTGAGAG
CAGCACCAGCTCCCCGTCTCAACATGAGGCCACTCCAGGGGCAAGGTTGCTGCTGCGAATCACCGAAAGAACATGGAGGA
AAGAAGAGAAGAACCTTCAGAAAGGACATGAAGTTGATTTTCAGAGCAGTATTAGAATAGAAGGTACAGAGGCTTCAGTT
GAGACCACAGGAGTTGACATCACTAAAATTCAAGTCAAGAGATGGGAGACCGTGAGAGAGATGCGCATGCAGAAACAGCA
GGAGAGGGAAAAATCAGTCTTGACACCTCTTCAGGGAGATGTAGCCTCTTGCAATACCCAAGTGGCAGAGAAACGAGTGC
TCACTGCTGGGCCAGGAATCACATGGCACCTGACCAAGCAGCTTCCCACAAAGTCATCCCAGAAGGTGGAGGTAGAAACC
TCAGGGATTGGACACTCATTATTGAATGTGAAATGTGCAGCACAGACCTTGGAAACAAGGGGTAAAGCTGAACCCAAAGT
GAACGTGAAGCAATCTGTGGTTAAAGTTGTGTCATCCCCCAAATTGGCCCCAAAACGTAAGGCAGTGGAGATGCACCCTG
CTGTCACTGCCGCTGTGAAGCCACTCAGCTCCAGCAGCGTCCTACAGGAACCCCCAGCCAAAAAGGCAGCTGTGGCTGTT
GTCCCGCTTGTCTCTGAGGACAAATCAGTCACTGTGCCTGAAGCAGAAAATCCTAGAGACAGTCTTGTGCTGCCTCCAAC
CCAGTCCTCTTCAGATTCCTCACCCCCGGAGGTGTCTGGCCCTTCCTCATCCCAAATGAGCATGAAAACTCGCCGACTCA
GCTCTGCCTCAACAGGAAAGCCCCCACTCTCTGTGGAGGATGATTTTGAGAAACTAACGTGGGAGATTTCAGGAGGCAAA
TTGGAAGTTGAGATTGACCTGGATCCTGGGAAAGATGAAGATGACCTTCCGCTTGAGCTATGAGAAATGATTGATAGC

Alignment

ORF - retro_ptro_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.78 %
• Parental protein coverage: 52.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSKTDDSTSGARSSSTIRIKTFSEVLAEKKHRQQEAERQKSKKDTTCIKLKIDSEIKKTVVLPPIVASRG
          PSKTDDSTSGARSSSTIRIKTFSEVLAE..HRQQEAERQKSKKDTTCIKLK.DSEIKKTVVLPPIVAS.G
Retrocopy PSKTDDSTSGARSSSTIRIKTFSEVLAEEEHRQQEAERQKSKKDTTCIKLKTDSEIKKTVVLPPIVASKG

Parental  QSEEPAGKTKSMQEVHIKTLEEIKLEKALRVQQSSESSTSSPSQHEATPGARRLLRITKRTGMKEEKNLQ
          QSEEPAGKTKSMQEVH.KTLEEIKLEKALRVQQSSESSTSSPSQHEATPGAR.LLRIT.RT..KEEKNLQ
Retrocopy QSEEPAGKTKSMQEVHMKTLEEIKLEKALRVQQSSESSTSSPSQHEATPGARLLLRITERTWRKEEKNLQ

Parental  EGNEVDSQSSIRTEAKEASGETTGVDITKIQVKRCETMREKHMQKQQEREKSVLTPLRGDVASCNTQVAE
          .G.EVD.QSSIR.E..EAS.ETTGVDITKIQVKR.ET.RE..MQKQQEREKSVLTPL.GDVASCNTQVAE
Retrocopy KGHEVDFQSSIRIEGTEASVETTGVDITKIQVKRWETVREMRMQKQQEREKSVLTPLQGDVASCNTQVAE

Parental  KPVLTAVPGITRHLTKRLPTKSSQKVEVETSGIGDSLLNVKCAAQTLEKRGKAKPKVNVKPSVVKVVSSP
          K.VLTA.PGIT.HLTK.LPTKSSQKVEVETSGIG.SLLNVKCAAQTLE.RGKA.PKVNVK.SVVKVVSSP
Retrocopy KRVLTAGPGITWHLTKQLPTKSSQKVEVETSGIGHSLLNVKCAAQTLETRGKAEPKVNVKQSVVKVVSSP

Parental  KLAPKRKAVEMHAAVIAAVKPLSSSSVLQEPPAKKAAVAVVPLVSEDKSVTVPEAENPRDSLVLPPTQSS
          KLAPKRKAVEMH.AV.AAVKPLSSSSVLQEPPAKKAAVAVVPLVSEDKSVTVPEAENPRDSLVLPPTQSS
Retrocopy KLAPKRKAVEMHPAVTAAVKPLSSSSVLQEPPAKKAAVAVVPLVSEDKSVTVPEAENPRDSLVLPPTQSS

Parental  SDSSPPEVSGPSSSQMSMKTRRLSSASTGKPPLSVEDDFEKLIWEISGGKLEAEIDLDPGKDEDDLLLEL
          SDSSPPEVSGPSSSQMSMKTRRLSSASTGKPPLSVEDDFEKL.WEISGGKLE.EIDLDPGKDEDDL.LEL
Retrocopy SDSSPPEVSGPSSSQMSMKTRRLSSASTGKPPLSVEDDFEKLTWEISGGKLEVEIDLDPGKDEDDLPLEL

Parental  SEMIDS
          .EMIDS
Retrocopy *EMIDS

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	0.20 RPM	80.24 RPM
SRP007412_cerebellum	0.00 RPM	108.37 RPM
SRP007412_heart	0.03 RPM	51.94 RPM
SRP007412_kidney	0.00 RPM	98.10 RPM
SRP007412_liver	0.00 RPM	55.68 RPM
SRP007412_testis	28.35 RPM	101.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_380 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_380 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_508

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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,