RetrogeneDB ID: retro_ptro_3228

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:65418358..65419129(-)
• Located in intron of: None

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_3228
TTAGCATTGGAGTCAAACCCTTCTGACCATCCAAGGGCAAGCACAATTTTCCTGCGCAAATCTCAAACGGATGTGAGAGA
AAAGAGGAAGAGCAACCATTTAAACCATGTATCTCCAGGGCAGCTTACTAAAAAGTATAGCTCATGCTCAACAATATTTC
TATATGACAGCACAGTCAACCAGCCTAACCTGAGAACCACAGTAAAATGTGTGACCTTAGCAATATATCACCACATAAAG
AACAGAGATGCAAATAGATCCCTGGATATTTTTGATGAGAGATCACATCCACTTACACGAGAAAAAGTTCCAGAAGAATA
GTTTAAGCATGATCCTGAGCACAAATTTATTTACAGATTTGTTCATACTCCTTTTAGTGCTGCACAGCTAACAGCTGAAT
GTGCAATAGTAACTTTGGTTTACTTAGAAAAGCTTTTAACTTATGCTGAAACCAACATTTGTCCCACTAACTGGAAAAGG
ATTGGTCTGCGAGCCATTCTTGCCTCCAAGGTTTGGGACCATCAGGCTGTATGGAATATGGACTACTGCCAGATCTTCAA
GGACATTACAGGTGAGGACATGAATGAAATGGAAAGGCATTTTTTGATGCTTCTTCAGTTTAATATTAATGTTCCTGCCA
GTGTTTATGCCAAATTAGTATTTGATCTTCGCTCCTTAGCAGATGACAATAACCTGAATTTTCTATTTGCTCCGCTTAGC
AAAAAAAGAGCACAGAACCTAGAGGCTATTTCTAGATTGTGTGAAGACAAA

Alignment

ORF - retro_ptro_3228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.23 %
• Parental protein coverage: 89.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LNMEFNPSDHPRASTIFLSKSQTDVREKRKSLFINHHPPGQIARKYSSCSTIFLDDSTVSQPNLKYTIKC
          L..E.NPSDHPRASTIFL.KSQTDVREKRKS...NH..PGQ...KYSSCSTIFL.DSTV.QPNL..T.KC
Retrocopy LALESNPSDHPRASTIFLRKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIFLYDSTVNQPNLRTTVKC

Parental  VALAIYYHIKNRDPDGRMLLDIFDENLHPLSKSEVPPDYDKHNPEQKQIYRFVRTLFSAAQLTAECAIVT
          V.LAIY.HIKNRD......LDIFDE..HPL....VP....KH.PE.K.IYRFV.T.FSAAQLTAECAIVT
Retrocopy VTLAIYHHIKNRDANRS--LDIFDERSHPLTREKVPEE*FKHDPEHKFIYRFVHTPFSAAQLTAECAIVT

Parental  LVYLERLLTYAEIDICPANWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNELERQFLELLQF
          LVYLE.LLTYAE..ICP.NWKRI.L.AIL.ASKVWD.QAVWN.DYCQI.KDIT.EDMNE.ER.FL.LLQF
Retrocopy LVYLEKLLTYAETNICPTNWKRIGLRAIL-ASKVWDHQAVWNMDYCQIFKDITGEDMNEMERHFLMLLQF

Parental  NINVPSSVYAKYYFDLRSLAEANNLSFPLEPLSRERAHKLEAISRLCEDK
          NINVP.SVYAK..FDLRSLA..NNL.F...PLS..RA..LEAISRLCEDK
Retrocopy NINVPASVYAKLVFDLRSLADDNNLNFLFAPLSKKRAQNLEAISRLCEDK

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	28.08 RPM
SRP007412_cerebellum	0.04 RPM	19.97 RPM
SRP007412_heart	0.12 RPM	25.85 RPM
SRP007412_kidney	0.13 RPM	26.10 RPM
SRP007412_liver	0.00 RPM	19.48 RPM
SRP007412_testis	0.32 RPM	194.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3228 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3228 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4845
Macaca mulatta	retro_mmul_2587

---

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,