RetrogeneDB ID: retro_ptro_1322

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:21831529..21832348(+)
• Located in intron of: ENSPTRG00000010763

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNY
• Ensembl ID: ENSPTRG00000002421
• Aliases: None
• Description: Cyclin Y [Source:UniProtKB/TrEMBL;Acc:K7BZJ5]

Sequence

>retro_ptro_1322
TTAGCTTTGGAGTCAAACCCTTCTGACCATCCAAGGGCAAGCACAAGTTTCCTGAGCAAATCTCAAACCGATGTGCGAGA
CAAGAGGAAGAGCAACCACTTAAATCATCTATCTCCAGGGCAGCTTACTAAAAAGTATAGCTCATGCTCAACAATATTTC
TAGGTGACAGAACAGTCAGCCAGCCTAACCTTAGAACCACAGTAAAATGTGTGACCTTAGAAATATATTACCGCATAAAG
AACAGAGACGCAAACAGATCCCTGGATATTTTTGGTGAGAGATCACATCCCCTCACACGAGAAAAAGTTCCACAGGAATA
GTTGAAGCATGATCCTGAGCACAAATTTATTTACAGATTTGTTCATACTCTTTTTAGTGCTGCACAGCTAACAGCTGAAT
GTGCAATAGTAACTCTGGTTTACTTAGAAAGGCTTTTAACTTATGCTGAAATCGACATTTGCCCCACTAACTGGAAAAGG
ATTGTTCTGGGAGCCACTCTTCTTGACTCCAAGGTTTGGGATGATCAGGCTGTATGGAATGTGGTCTACTGCCAGATCCT
CAAGGACATTACAGTTGAGGACATGAATGAAATGGAAAGGCATTTTTCGGAGCTTCTTCAGTTTAATATTAATGTTCCTG
CCAGTGTTTATGCCAAACACTACCTTGACCTTCGCTCCTTAGCAGATGACAACCTGAATTTTCTATTTGCTCCTCTTAGC
AAAGAAAGAGCACAGAACCTAGAGGCTATTTCTAGGTTATGTGAAGACAAAGACTTGTGTGGAGCAGCTGTAAGAAGGTC
TTTCAGCGCTGATCAACTT

Alignment

ORF - retro_ptro_1322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.46 %
• Parental protein coverage: 96.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LNMEFNPSDHPRASTIFLSKSQTDVREKRKSLFINHHPPGQIARKYSSCSTIFLDDSTVSQPNLKYTIKC
          L..E.NPSDHPRAST.FLSKSQTDVR.KRKS...NH..PGQ...KYSSCSTIFL.D.TVSQPNL..T.KC
Retrocopy LALESNPSDHPRASTSFLSKSQTDVRDKRKSNHLNHLSPGQLTKKYSSCSTIFLGDRTVSQPNLRTTVKC

Parental  VALAIYYHIKNRDPDGRMLLDIFDENLHPLSKSEVPPDYDKHNPEQKQIYRFVRTLFSAAQLTAECAIVT
          V.L.IYY.IKNRD......LDIF.E..HPL....VP....KH.PE.K.IYRFV.TLFSAAQLTAECAIVT
Retrocopy VTLEIYYRIKNRDANRS--LDIFGERSHPLTREKVPQE*LKHDPEHKFIYRFVHTLFSAAQLTAECAIVT

Parental  LVYLERLLTYAEIDICPANWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNELERQFLELLQF
          LVYLERLLTYAEIDICP.NWKRIVLGA.LL.SKVWDDQAVWNV.YCQILKDITVEDMNE.ER.F.ELLQF
Retrocopy LVYLERLLTYAEIDICPTNWKRIVLGATLLDSKVWDDQAVWNVVYCQILKDITVEDMNEMERHFSELLQF

Parental  NINVPSSVYAKYYFDLRSLAEANNLSFPLEPLSRERAHKLEAISRLCEDKYKDLRRSARKRSASADNL
          NINVP.SVYAK.Y.DLRSLA...NL.F...PLS.ERA..LEAISRLCED..KDL...A..RS.SAD.L
Retrocopy NINVPASVYAKHYLDLRSLAD-DNLNFLFAPLSKERAQNLEAISRLCED--KDLCGAAVRRSFSADQL

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	28.08 RPM
SRP007412_cerebellum	0.07 RPM	19.97 RPM
SRP007412_heart	0.00 RPM	25.85 RPM
SRP007412_kidney	0.05 RPM	26.10 RPM
SRP007412_liver	0.00 RPM	19.48 RPM
SRP007412_testis	1.79 RPM	194.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1322 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1322 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1984

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006201	1 retrocopy	retro_chof_2504,
Echinops telfairi	ENSETEG00000005121	1 retrocopy	retro_etel_2021,
Loxodonta africana	ENSLAFG00000012820	1 retrocopy	retro_lafr_79,
Pan troglodytes	ENSPTRG00000002421	2 retrocopies	retro_ptro_1322 , retro_ptro_3228,
Pan troglodytes	ENSPTRG00000008072	1 retrocopy	retro_ptro_1091,