RetrogeneDB ID: retro_ptro_2924

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03150515.1:2743..3376(-)
• 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_2924
ATGTGAGCTCATACATCCACGATTGAAAATAATGCATGAAGATCAATTAATCAAAGAAGTCTTGGATAAATTCCCTAATT
GTCATGAGCAAACATATGATTAAGAATTTCTGAACACTTTTACTCATCTTTCACAAGAGGATCTTGTGTCCAAAAGGGGA
GTGTTTGGAACTGATTCTTCAGAAAACATTTTTACCTAAGCAAAAGTTACTCATAAAAATGAAGCTAATGACTACCATCT
TAGAAATAAAACCATTTTTCTTCGTACTTCATCACAATGTTTGGAAGAACAGGTAGAAAATTTCCTAGATTTGGAAGATT
TGGACATGGATGAAGAGATTAAACCCCAAATAAGTGAGGATTTGCTGCTGCTCCCAGGAGAAGTGGAGTAGGATGTAAGC
ACCAGCATTCCTTCCTGTATCCTTCTGTGGCCCAGCCTCCCACCTGTGAAGTGAAGCCAAAGCCTACTGTAAAAAGAATG
GACAAACAGATGGAAGAGATATGTGGAGATGAAGCTCAACCCTTCTCACTTGATGAGGAATTCGATTATGACAATGTGAC
GCTAACCTCCAAGTTTAGTCCTGCAGAGACACAGACCATCAAAGAGCTAGGCAAGCAGAAGAGAAAGGACACC

Alignment

ORF - retro_ptro_2924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.45 %
• Parental protein coverage: 95.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSAHMSGLE-IMDEDQLIKDVLDKFLNCHEQTYDEEFLNTFTHLSQEDHVSTRGVFGTDSSENICTSAKV
          M.AH.S..E.IM.EDQLIK.VLDKF.NCHEQTYD.EFLNTFTHLSQED.VS.RGVFGTDSSENI.T.AKV
Retrocopy M*AHTSTIE>IMHEDQLIKEVLDKFPNCHEQTYD*EFLNTFTHLSQEDLVSKRGVFGTDSSENIFT*AKV

Parental  THKNEADDYHLRNKTIFLHTSSQCLEEQVDNFLDLEDLDMDEEIKPQMSEDLLLLPGEVEQDVSTSIPSC
          THKNEA.DYHLRNKTIFL.TSSQCLEEQV.NFLDLEDLDMDEEIKPQ.SEDLLLLPGEVE.DVSTSIPSC
Retrocopy THKNEANDYHLRNKTIFLRTSSQCLEEQVENFLDLEDLDMDEEIKPQISEDLLLLPGEVE*DVSTSIPSC

Parental  I-PFVAQPPTCEVKPKPTVKRMDKQTEEILGDEVQPFSLDEEFDYDNVTLTSKFSPTEIENIKELCKQQK
          I.P.VAQPPTCEVKPKPTVKRMDKQ.EEI.GDE.QPFSLDEEFDYDNVTLTSKFSP.E...IKEL.K.QK
Retrocopy I<PSVAQPPTCEVKPKPTVKRMDKQMEEICGDEAQPFSLDEEFDYDNVTLTSKFSPAETQTIKELGK-QK

Parental  RKDT
          RKDT
Retrocopy RKDT

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	0.00 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_2924 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2924 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2924 has 0 orthologous retrocopies within eutheria group .

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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,