RetrogeneDB ID: retro_ptro_2962

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03190007.1:1369..2198(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC7
• Ensembl ID: ENSPTRG00000020939
• Aliases: None
• Description: zinc finger, CCHC domain containing 7 [Source:HGNC Symbol;Acc:26209]

Sequence

>retro_ptro_2962
AAGAGCACCATTTCAGAAGGCAATAATGTGGAAAGCTGGATGCTACTGGGATGTGAAGTAGATGATAAAGATAATGATAT
CCTTCTCAACCTTCTGGGATGTGAAAACTCTGTTACTGAAGGAGAAGATGGTATAAACTGGTTCATCAGTGACAAAGACA
TTGAGGCCCAGATAGCTAATAACCAATAACCTGGAAGATGGACCCAGCGATATTATTCAGCCAATGAAAATATTATCTGT
AGAAATTGTGACAAACGCGGCCATTTATCAAAAAACCGTCCCTTACCATGAAAAGTTCGTTGCTGCTTCCTGTGCTCCAG
GAGAGGACACCTCCTGTATTCCTGTCCAGCCCCCCTTTGCAAATACTGTCCTGTGCCTAAGATGTTGGACCACTCATGTC
TTTTCAGACATTCTTGGGATAAACAGTGTGACCAATGTCATATGCTAGGCCACTATACAGATGCTTGCACAGAAATCTGG
AGGCAATATCACCTCACAACCAAACCCAGACCACCCAAAAAGCTGAAGACCCTTCAAAACCATCAGCCTTAGCATATTGC
TGTCACTGCATGCAAAAGGCCATTATGGACACAAGTGTCCAGAAAGAGAAGTGTATGACCTGTCTCCAGTATCTCCATTC
ATCTGCTACTATGATGACAAATATGAAGTTAAGGAGAGAAAAAAGAGAGTAAAATAAAAAATAAAAGTACTCAAGGAGAG
TGGGGATATCCCAGAGCCATCCAAGCTACCTTACATAAAAGCAGCAAATGAGAACCCCCATCATGATATAAAGAAGGGCT
GTGGCTCGTGGAAAAGCAACAGGTGGCCT

Alignment

ORF - retro_ptro_2962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.44 %
• Parental protein coverage: 62.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESSSSKPNQKKLIVLSDSEVIQLSDGSEVITLSDEDSIYRCKGEDGINWFISDKDIEAQIANNRTPGRWT
          .S..S..N......L...EV...........L..E.S.....GEDGINWFISDKDIEAQIANN..PGRWT
Retrocopy KSTISEGNNVESWMLLGCEVDDKDNDILLNLLGCENSV--TEGEDGINWFISDKDIEAQIANNQ*PGRWT

Parental  QRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHS
          QRYYSAN.NIICRNCDKRGHLSKN.PLP.KVR.CFLCSRRGHLLYSCPAPLC.YCPVPKMLDHSCLFRHS
Retrocopy QRYYSANENIICRNCDKRGHLSKNRPLP*KVRCCFLCSRRGHLLYSCPAPLCKYCPVPKMLDHSCLFRHS

Parental  WDKQCDRCHMLGHYTDAGTEIWRQYHLTTKPGPPKKPKT-PSRPSALAYCYHCAQ-KGHYGHECPEREVY
          WDKQCD.CHMLGHYTDA.TEIWRQYHLTTKP.PPKK.KT.PS.PSALAYC.HC.Q.KGHYGH.CPEREVY
Retrocopy WDKQCDQCHMLGHYTDACTEIWRQYHLTTKPRPPKKLKT<PSKPSALAYCCHCMQ<KGHYGHKCPEREVY

Parental  DPSPVSPFICYYDDKYEIQEREKRLKQKIKVLKKNGVIPEPSKLPYIKAANENPHHDIRKGRASWKSNRW
          D.SPVSPFICYYDDKYE..E..........VLK..G.IPEPSKLPYIKAANENPHHDI.KG..SWKSNRW
Retrocopy DLSPVSPFICYYDDKYEVKEXXXXXXXXXXVLKESGDIPEPSKLPYIKAANENPHHDIKKGCGSWKSNRW

Parental  P
          P
Retrocopy P

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	4.65 RPM
SRP007412_cerebellum	0.00 RPM	8.17 RPM
SRP007412_heart	0.00 RPM	4.20 RPM
SRP007412_kidney	0.00 RPM	5.94 RPM
SRP007412_liver	0.00 RPM	6.97 RPM
SRP007412_testis	0.00 RPM	20.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2962 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2962 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147905	1 retrocopy	retro_hsap_1342,
Macaca mulatta	ENSMMUG00000007421	1 retrocopy	retro_mmul_2180,
Pongo abelii	ENSPPYG00000029763	1 retrocopy	retro_pabe_1114,
Pan troglodytes	ENSPTRG00000020939	2 retrocopies	retro_ptro_2962 , retro_ptro_917,
Tursiops truncatus	ENSTTRG00000006054	2 retrocopies	retro_ttru_1606, retro_ttru_505,