RetrogeneDB ID: retro_ptro_320

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:90087470..90088129(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf74
• Ensembl ID: ENSPTRG00000003514
• Aliases: None
• Description: chromosome 11 open reading frame 74 [Source:HGNC Symbol;Acc:25142]

Sequence

>retro_ptro_320
ATGTGGGCTCATACATCAGGATTGAAAATAATGCACGAAGATCAATTAATCAAAGAAGTCTTGGATAAATTCCTTAATTG
TCATGAGCAAACATATGATTAAGAATTTCTGAACACTTTTACTCATCTTTCACAAGAGGATCTTGTGTCCAAAAGGGGAG
TGTTTGGAACTGATTCTTCAGAAAACATTTTTACCTAAGCAAAAGTTACTCATAAAAATGAAGCTAATGACTACCATCTT
AGAAATAAAACCATTTTTCTTCGTACTTCATCACAATGTTTGGAAGAACAGGTAGACAATTTCCTAGATTTGGAAGATTT
GGACATGGATGAAGAGATTAAACCCCAAATAACTGAGGATTTGCTGCTGCTCCCAGGAGAAGTGGAGTAGGATGTAAGCA
CCAGCATTCCTTCCTGTATCCTTCTGTGGCCCAGCCTCCCACCTGTGAAGTGAAGCCAAAGCCTACTGTAAAAAGAATGG
ACAAACAGATGGAAGAGATATGTGGAGATGAAGCTCAACCCTTCTCACTTGATGAGGAATTCGATTATGACAATGTGACG
CTAACCTCCAAGTTTAGTCCTGCAGAGACAGAGACCATCAAAGAGCTAGGCAAGCAGAAGAGAAAGGACACCAGCCCAGA
CTTACAGGAACCCTGTGAC

Alignment

ORF - retro_ptro_320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAHMSGLEIMDEDQLIKDVLDKFLNCHEQTYDEEFLNTFTHLSQEDHVSTRGVFGTDSSENICTSAKVT
          M.AH.SGL.IM.EDQLIK.VLDKFLNCHEQTYD.EFLNTFTHLSQED.VS.RGVFGTDSSENI.T.AKVT
Retrocopy MWAHTSGLKIMHEDQLIKEVLDKFLNCHEQTYD*EFLNTFTHLSQEDLVSKRGVFGTDSSENIFT*AKVT

Parental  HKNEADDYHLRNKTIFLHTSSQCLEEQVDNFLDLEDLDMDEEIKPQMSEDLLLLPGEVEQDVSTSIPSCI
          HKNEA.DYHLRNKTIFL.TSSQCLEEQVDNFLDLEDLDMDEEIKPQ..EDLLLLPGEVE.DVSTSIPSCI
Retrocopy HKNEANDYHLRNKTIFLRTSSQCLEEQVDNFLDLEDLDMDEEIKPQITEDLLLLPGEVE*DVSTSIPSCI

Parental  -PFVAQPPTCEVKPKPTVKRMDKQTEEILGDEVQPFSLDEEFDYDNVTLTSKFSPTEIENIKELCKQQKR
          .P.VAQPPTCEVKPKPTVKRMDKQ.EEI.GDE.QPFSLDEEFDYDNVTLTSKFSP.E.E.IKEL.K.QKR
Retrocopy <PSVAQPPTCEVKPKPTVKRMDKQMEEICGDEAQPFSLDEEFDYDNVTLTSKFSPAETETIKELGK-QKR

Parental  KDTSPDLKKSCD
          KDTSPDL...CD
Retrocopy KDTSPDLQEPCD

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	7.40 RPM
SRP007412_cerebellum	0.00 RPM	2.04 RPM
SRP007412_heart	0.00 RPM	7.87 RPM
SRP007412_kidney	0.00 RPM	7.19 RPM
SRP007412_liver	0.03 RPM	1.64 RPM
SRP007412_testis	0.00 RPM	26.03 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_320 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_320 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_418
Gorilla gorilla	retro_ggor_411
Pongo abelii	retro_pabe_302

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000010963	2 retrocopies	retro_dord_388, retro_dord_615,
Homo sapiens	ENSG00000166352	1 retrocopy	retro_hsap_418,
Gorilla gorilla	ENSGGOG00000004773	1 retrocopy	retro_ggor_411,
Macropus eugenii	ENSMEUG00000003065	1 retrocopy	retro_meug_328,
Microcebus murinus	ENSMICG00000008620	1 retrocopy	retro_mmur_383,
Monodelphis domestica	ENSMODG00000019838	1 retrocopy	retro_mdom_1594,
Pongo abelii	ENSPPYG00000003347	1 retrocopy	retro_pabe_302,
Pan troglodytes	ENSPTRG00000003514	2 retrocopies	retro_ptro_2924, retro_ptro_320 ,
Tupaia belangeri	ENSTBEG00000004277	2 retrocopies	retro_tbel_2155, retro_tbel_2277,