RetrogeneDB ID: retro_ptro_1269

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:56290676..56291516(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2H1
• Ensembl ID: ENSPTRG00000003420
• Aliases: None
• Description: None

Sequence

>retro_ptro_1269
ATGGCAACCTCCTCTGAAGAAGTTTTGCTGATTGTAAAGAAAGTGCGTCAAAAGAAGCAGGATGGAGCTCTATACCTCAT
GGCAGAAAGAATTGCTTGGGCACCTGAAGGCAAAAATAGATTTACAGTCAGCCGTATGTATGTAGATGTTAAATGCCAGA
AAATTAGTCCAGAAGGCAAAGCTACAATTTAGCATCAGCTGGACCTACATGCAGGAGATGCAATTAACTTCTGTTTTCCC
AATGAAAACACAGCAGTGAAAGAGCAAGATGCAGTAAAGGACCTTCAGCAGCTGCTGCCCAAATTCAAGAGGAAAGCAAA
TAAAGAACTGGAAGAGAAGAACAGAATGCTGCAAGAAGATCCTGTTTTGTTTCAGCTTTATAAAGATCTTCTTGTGAGCC
AAGTGTTGAGTGCTGAGGAATTCTCGGCCAATCATTTAAATGGGAATGCAACAGAAAATTCTTACACATCCAATCATAAG
CAGGATGTTGGCATTTCTGCTGCATATCTGGCTGATGTCTGGCCCGAAATCGATGGCTGTAATGGTCTGAGATATAATTT
AACTTCTGATATCATTGAGTTCATATTTAGGACCTATCCAGCAGTGAAAATGAAATATGCAGAAAGTGTTCCCCACAACA
TGACAGAGAAGGGATTCTGGACACGTTTTTTCCAGTCCCATTATTTTCACAGGGATCGGCTGAATACAGGGTCAAAGGAT
CTCTCTGCAGAATGTGCCAAAATAGATGAAAAGGGCCTTAAAACAATGGTTTCATTAGGAGTGAAAAACCCACTACTAGA
ATTAACAGCTTTGGGAAATAAACCAGAGTCCAGTGAATAT

Alignment

ORF - retro_ptro_1269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.12 %
• Parental protein coverage: 51.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLH
          MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGK.RFT.S.MY.D.KCQKISPEGKA.I..QL.LH
Retrocopy MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKNRFTVSRMYVDVKCQKISPEGKATI*HQLDLH

Parental  AGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVISAE
          AGD..NF.F.NE.TAVKE.DAVKD.LQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDL.VSQV.SAE
Retrocopy AGDAINFCFPNENTAVKEQDAVKD-LQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLLVSQVLSAE

Parental  EFWANRLNVNATDSSSTSNHKQDVGISAAFLADVRPQTDGCNGLRYNLTSDIIESIFRTYPAVKMKYAEN
          EF.AN.LN.NAT..S.TSNHKQDVGISAA.LADV.P..DGCNGLRYNLTSDIIE.IFRTYPAVKMKYAE.
Retrocopy EFSANHLNGNATENSYTSNHKQDVGISAAYLADVWPEIDGCNGLRYNLTSDIIEFIFRTYPAVKMKYAES

Parental  VPHNMTEKEFWTRFFQSHYFHRDRLNTGSKDLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEG
          VPHNMTEK.FWTRFFQSHYFHRDRLNTGSKDL.AECAKIDEKGLKTMVSLGVKNPLL.LTAL..KP....
Retrocopy VPHNMTEKGFWTRFFQSHYFHRDRLNTGSKDLSAECAKIDEKGLKTMVSLGVKNPLLELTALGNKPESSE

Parental  Y
          Y
Retrocopy Y

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	22.29 RPM
SRP007412_cerebellum	0.00 RPM	28.68 RPM
SRP007412_heart	0.00 RPM	15.39 RPM
SRP007412_kidney	0.00 RPM	24.97 RPM
SRP007412_liver	0.00 RPM	17.48 RPM
SRP007412_testis	0.00 RPM	99.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1269 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1269 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1269 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110768	1 retrocopy	retro_hsap_1892,
Gorilla gorilla	ENSGGOG00000008405	1 retrocopy	retro_ggor_1385,
Monodelphis domestica	ENSMODG00000006540	1 retrocopy	retro_mdom_1210,
Nomascus leucogenys	ENSNLEG00000017760	1 retrocopy	retro_nleu_1473,
Otolemur garnettii	ENSOGAG00000000710	1 retrocopy	retro_ogar_338,
Pan troglodytes	ENSPTRG00000003420	1 retrocopy	retro_ptro_1269 ,