RetrogeneDB ID: retro_ptro_2824

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:35874960..35875423(+)
• Located in intron of: None

Retrocopy information

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

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_2824
AGCCAACCTGCAACCTCTGAATCTTTACCAGTTCAATGCACAGATGGCAGTGTCCCAGAAGCCCAGTCAACATTAGACTC
TACATCTTCATCTATGCAGCCAAGCCCTGTATCAAATCAGTCACTTTTATCAGAATCTGTAGCATCTTCTCAATTGGACA
GTACATCTGTGGACAAGCAGTACCTGAAACAGAAGATCTGCAGGCTTCAGTATCAGACATGGCACAGCAGCCATCTGAAG
AGCAAAGCAAGTCTCTTGAAAAACCAAAACAAAAAAAGAATCTCTGTTTCATGTGCAGCAAGAAAGTGGGACTTACTAGG
TTTGAATGCGGTGTAGAAATGTTTACTGTGGTGTACACTGTTACTCAGATCTACACAATTGCTCTTAAAATTACAAAGCT
GATGCCGCTGAGAAAATCAGAAAAGAAAATCCAGTAGTTGTTGGCTAGAAGATCCAAAAGATT

Alignment

ORF - retro_ptro_2824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.35 %
• Parental protein coverage: 74.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVSSLSESLPVQCTDGSVPEAQSTLDSTSSSMQPSPVSNQSLLSESVASSQLDSTSVDK-AVPETEDVQA
          S....SESLPVQCTDGSVPEAQSTLDSTSSSMQPSPVSNQSLLSESVASSQLDSTSVDK.AVPETED.QA
Retrocopy SQPATSESLPVQCTDGSVPEAQSTLDSTSSSMQPSPVSNQSLLSESVASSQLDSTSVDK<AVPETEDLQA

Parental  SVSDTAQQPSEEQSKSLEKPKQKKNRCFMCRKKVGLTGFEC-RCGNVYCGVHRYSDVHNCSYNYKADAAE
          SVSD.AQQPSEEQSKSL.......N.CFMC.KKVGLT.FEC.RC.NVYCGVH.YSD.HNCS.NYKADAAE
Retrocopy SVSDMAQQPSEEQSKSLXXXXXXXNLCFMCSKKVGLTRFEC<RCRNVYCGVHCYSDLHNCS*NYKADAAE

Parental  KIRKENPVVVGEKIQKI
          KIRKENPVVVG.KIQKI
Retrocopy KIRKENPVVVG*KIQKI

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	0.02 RPM	16.39 RPM
SRP007412_cerebellum	0.00 RPM	17.24 RPM
SRP007412_heart	0.00 RPM	33.84 RPM
SRP007412_kidney	0.00 RPM	35.23 RPM
SRP007412_liver	0.03 RPM	24.26 RPM
SRP007412_testis	2.32 RPM	116.45 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2824 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2824 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4153
Gorilla gorilla	retro_ggor_2790

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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,