RetrogeneDB ID: retro_ptro_1375

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:47560530..47561170(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000038866
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZFAND6
• Ensembl ID: ENSPTRG00000007361
• Aliases: None
• Description: Pan troglodytes zinc finger, AN1-type domain 6 (ZFAND6), mRNA. [Source:RefSeq mRNA;Acc:NM_001246634]

Sequence

>retro_ptro_1375
ATGGCTCAGGAGACTAACCAGACCCCGGGGCCCATGCTGTGTAGCACAGGATGTGGCTTTTATGGAAATCCTAGGACAAA
TGGAATGTGTTCAGTCTGCTACAAAGAACATCTTCAGAGGCAGCAGAATAGTGGCAGAATGAGCCCAATGGGGACAGCTA
GTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAGAGAGCAGACACTAGCTTAAACAACTGTGAAGGTGCTGCT
GGCAGCACATCTGAAAAATCAAGAAATGTGCCTGCGGCTGCCTTGCCTGTAACTCAGCAAATGACAGAAATGAGCATTTC
AACAGAGGACAAAATAACTACCCCGAAAACAGAGGTGTGAGAGCCAGTTGTCACTCAGCCCAGTCCATCAGTTTTTCAGC
CCAGTACTTCTCAGAGTGAAGAAAAAGCTCCTGAATTGCCCAAACCAAAGAAAAACAGATGTTTCATGTGCAGAAAGAAA
GTTGGTCTTACAGGGTTTGACTGCCGATGTGGAAATTTGTTTTGTGGACTTCACCGTTAACTCTGACAAGCACAACTGTC
CATATGATTACAAAGCAGAAGCTGCAGCAAAAATTAGAAAAGAGAATCCAGTTGTTGTGGCTGAAAAAATTCAGAGAATA

Alignment

ORF - retro_ptro_1375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQETNHSQVPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQNSSNGRISPPAT---SVSSLSESLPVQCT
          MAQETN....PMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQ..S.GR.SP..T...S.S..S.S..VQ..
Retrocopy MAQETNQTPGPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQQNS-GRMSPMGTASGSNSPTSDSASVQRA

Parental  DGSVPEAQSTLDSTSSSMQPSPVSNQSLLSESVASSQLDSTSVDKAVPET-EDVQASVSDTAQQPSEEQS
          D.S.........STS......P.............S............E..E.V....S....QPS..QS
Retrocopy DTSLNNCEGAAGSTSEKSRNVPAAALPVTQQMTEMSISTEDKITTPKTEV*EPVVTQPSPSVFQPSTSQS

Parental  --KSLEKPKQKKNRCFMCRKKVGLTGFECRCGNVYCGVHR-YSDVHNCSYNYKADAAEKIRKENPVVVGE
          ..K..E.PK.KKNRCFMCRKKVGLTGF.CRCGN..CG.HR..SD.HNC.Y.YKA.AA.KIRKENPVVV.E
Retrocopy EEKAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHR>NSDKHNCPYDYKAEAAAKIRKENPVVVAE

Parental  KIQKI
          KIQ.I
Retrocopy KIQRI

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	6.54 RPM	16.39 RPM
SRP007412_cerebellum	6.17 RPM	17.24 RPM
SRP007412_heart	4.17 RPM	33.84 RPM
SRP007412_kidney	5.60 RPM	35.23 RPM
SRP007412_liver	5.79 RPM	24.26 RPM
SRP007412_testis	3.79 RPM	116.45 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1375 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1375 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1375 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2063
Gorilla gorilla	retro_ggor_1485
Pongo abelii	retro_pabe_1676

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012321	1 retrocopy	retro_btau_593,
Choloepus hoffmanni	ENSCHOG00000009491	2 retrocopies	retro_chof_1516, retro_chof_2072,
Felis catus	ENSFCAG00000012931	2 retrocopies	retro_fcat_1024, retro_fcat_1998,
Homo sapiens	ENSG00000086666	1 retrocopy	retro_hsap_4153,
Gorilla gorilla	ENSGGOG00000015621	1 retrocopy	retro_ggor_2790,
Loxodonta africana	ENSLAFG00000006722	1 retrocopy	retro_lafr_587,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685,
Nomascus leucogenys	ENSNLEG00000008870	1 retrocopy	retro_nleu_1387,
Pan troglodytes	ENSPTRG00000007361	2 retrocopies	retro_ptro_1375 , retro_ptro_2824,
Rattus norvegicus	ENSRNOG00000013506	1 retrocopy	retro_rnor_2019,
Sus scrofa	ENSSSCG00000001779	2 retrocopies	retro_sscr_1206, retro_sscr_1207,