RetrogeneDB ID: retro_ptro_2331

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:27528652..27529419(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA7
• Ensembl ID: ENSPTRG00000012645
• Aliases: None
• Description: cell division cycle associated 7 [Source:HGNC Symbol;Acc:14628]

Sequence

>retro_ptro_2331
GAAAGGGCTTGAAATATAAAGCAAAACAAAGCAATGCTTGTAAAACGCATGTCAGTATTAGAAGCTTCTCTGGTTTGTTC
CCTGGAAGACATTCCCCGCCAGGCCCCAACTCACAATCAAGGAGACCCCAAGGTAAACATTCCTGGATGTTGCTTCAAGA
AGACATTCTGAATGGAGAGAGCTCGGCCTCTTAGAAGTCAAGGTCAGGATCCTCGGGTCCCTTGGCGCTCTACCTACGGA
AGAGAAGGAAGAAAAGACAGAGGCTAAGTACATGTTGGTGAGAAAGAGTAAGATTGTGGACGGCTACATGAACGAAGTTG
AGATGCTCAGAAATCGTCCCGCCAGATCACCCATGATCCTTCCGCATATAATTCGCCCACCGGAAGAAATTACAGAGGAA
GGTTTGGAGAACATCTGCAGCAACTCTCAAGAGAAGATATATAACCGTTCGCTGGGTTCTATTTGTCATCAATGCCGCCA
GAAAACTATTGTTATCAAACAAACTGCAGAAACCCAGACTGTTGGGGCTTTCAAGGCCTGTTCTGCGGCCCCGACCTTAG
AAACCCTTGTGGTGAAGAGGTCAGGAATGCTCTGCTGGATGCGAACTGGCATTGTCCGCCTTGTTGAGGCCGTGCAACTG
CAGTTTCCGCTCGCAGCGAGATAGACTGTGGGGAACTGGGGTCCTTGAATATTTAGCCAAATACAATGGCTTTGGGAATG
TGCATGCTTACTTGAAAAGTCTGAAACAGGAATTTGAAATGCAAGCA

Alignment

ORF - retro_ptro_2331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.26 %
• Parental protein coverage: 57.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KRALNIKQNKAMLAKLMSELE-SFPGSFRGRHPLPGSDSQSRRPR-RRTFPGVASRRNPERRARPLTRSR
          .RA.NIKQNKAML.K.MS.LE.SF.G.F.GRH..PG..SQSRRP..R.TF..VASRR..E.R...L....
Retrocopy ERA*NIKQNKAMLVKRMSVLE<SFSGLFPGRHSPPGPNSQSRRPQ<R*TFLDVASRRHSEWRELGLLEVK

Parental  SRILGSLDALPMEEEEE--EDKYMLVRKRKTMDGYMNEDDLPRSRRSRSSVTLPHIIRPVEEITEEELEN
          .RILGSL.ALP.EE.EE..E.KYMLVRK.K..DGYMNE....R.R..RS...LPHIIRP.EEITEE.LEN
Retrocopy VRILGSLGALPTEEKEEKTEAKYMLVRKSKIVDGYMNEVEMLRNRPARSPMILPHIIRPPEEITEEGLEN

Parental  VCSNSREKIYNRSLGSTCHQCRQKTIDTK-TNCRNPDCWGVRGQFCGPCLRNRYGEEVRDALLDPNWHCP
          .CSNS.EKIYNRSLGS.CHQCRQKTI..K.TNCRNPDCWG..G.FCGP.LRN..GEEVR.ALLD.NWHCP
Retrocopy ICSNSQEKIYNRSLGSICHQCRQKTIVIK<TNCRNPDCWGFQGLFCGPDLRNPCGEEVRNALLDANWHCP

Parental  PCRG-ICNCSFCRQRDGRCATGVLVYLAKYHGFGNVHAYLKSLKQEFEMQA
          PC.G..CNCSF..QRD....TGVL.YLAKY.GFGNVHAYLKSLKQEFEMQA
Retrocopy PC*G<PCNCSFRSQRDRLWGTGVLEYLAKYNGFGNVHAYLKSLKQEFEMQA

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	0.20 RPM
SRP007412_cerebellum	0.00 RPM	0.36 RPM
SRP007412_heart	0.00 RPM	0.26 RPM
SRP007412_kidney	0.00 RPM	0.13 RPM
SRP007412_liver	0.00 RPM	0.23 RPM
SRP007412_testis	0.95 RPM	14.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2331 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2331 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2331 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3438

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007809	1 retrocopy	retro_cjac_4087,
Cavia porcellus	ENSCPOG00000011784	2 retrocopies	retro_cpor_661, retro_cpor_691,
Homo sapiens	ENSG00000144354	1 retrocopy	retro_hsap_3438,
Mus musculus	ENSMUSG00000055612	2 retrocopies	retro_mmus_1493, retro_mmus_1494,
Nomascus leucogenys	ENSNLEG00000005787	1 retrocopy	retro_nleu_2295,
Pan troglodytes	ENSPTRG00000012645	1 retrocopy	retro_ptro_2331 ,
Ictidomys tridecemlineatus	ENSSTOG00000009026	1 retrocopy	retro_itri_369,