RetrogeneDB ID: retro_ptro_1538

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:38354586..38355195(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRAP
• Ensembl ID: ENSPTRG00000004734
• Aliases: None
• Description: None

Sequence

>retro_ptro_1538
AAAAGGCTCCTATGGTGCAGTGAGGATAAACAGATTCTTTCTGCTGATGACAAAACTTCTCGACTTTGGGATCATGCTAC
TATGACAGAAGTGAAATCTCTAAATTTTAATATGTCTGTTAGTAGTACAAAATACATTCCTGAGGGAGAGATTTTGGTTA
TAACTTGTGGACTATCTATTGCTTTTCATAGTGCAGTAAGTTTGGACCCAATTACATCCTTTGAAGCTCCTGCAACCATC
AATTCTGCATCTCTTCATCCTGAGAAAGAATTTCTTGTTGCAGGTGGTGAAGATTTTAAACTTTATAAGTATTTTAACCA
TGGAGAAGAATTCGAATCCTACAAGGGATACTTTGGTCCTATTCACTGTGTGAGATTTAGTCGTGATGGAGAACTCTATG
CCAGTGGTTCTGAAGATAGAACATTGAGACTAGGGCAAACTGTGGTAGGAAAAACATACGGCCTTTGGAAATGTGTGCTT
CCTGAAGAAGAGAGTGGTGAGCTAGCAAAGCCAAAGATTGGCTTTCCAGAGACAACAGAAGAGGAGCTAGAAGAAATTGT
TTCAGAGAACTCAGATTGCATCTATTCTTCAACTCCTGATGTTAAGGCC

Alignment

ORF - retro_ptro_1538 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.71 %
• Parental protein coverage: 58.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKALWCSEDKQILSADDKTVRLWDHATMTEVKSLNFNMSVSSMEYIPEGEILVITYGRSIAFHSAVSLDP
          K..LWCSEDKQILSADDKT.RLWDHATMTEVKSLNFNMSVSS..YIPEGEILVIT.G.SIAFHSAVSLDP
Retrocopy KRLLWCSEDKQILSADDKTSRLWDHATMTEVKSLNFNMSVSSTKYIPEGEILVITCGLSIAFHSAVSLDP

Parental  IKSFEAPATINSASLHPEKEFLVAGGEDFKLYKYDYNSGEELESYKGHFGPIHCVRFSPDGELYASGSED
          I.SFEAPATINSASLHPEKEFLVAGGEDFKLYKY..N.GEE.ESYKG.FGPIHCVRFS.DGELYASGSED
Retrocopy ITSFEAPATINSASLHPEKEFLVAGGEDFKLYKY-FNHGEEFESYKGYFGPIHCVRFSRDGELYASGSED

Parental  GTLRLWQTVVGKTYGLWKCVLPEEDSGELAKPKIGFPETTEEELEEIASENSDCIFPSAPDVKA
          .TLRL.QTVVGKTYGLWKCVLPEE.SGELAKPKIGFPETTEEELEEI.SENSDCI..S.PDVKA
Retrocopy RTLRLGQTVVGKTYGLWKCVLPEEESGELAKPKIGFPETTEEELEEIVSENSDCIYSSTPDVKA

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	62.63 RPM
SRP007412_cerebellum	0.00 RPM	56.03 RPM
SRP007412_heart	0.03 RPM	60.10 RPM
SRP007412_kidney	0.00 RPM	61.82 RPM
SRP007412_liver	0.00 RPM	42.06 RPM
SRP007412_testis	0.00 RPM	71.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1538 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1538 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2092
Gorilla gorilla	retro_ggor_1633
Pongo abelii	retro_pabe_2005

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007422	2 retrocopies	retro_chof_1098, retro_chof_1620,
Callithrix jacchus	ENSCJAG00000021593	1 retrocopy	retro_cjac_2503,
Homo sapiens	ENSG00000023734	2 retrocopies	retro_hsap_2092, retro_hsap_3723,
Gorilla gorilla	ENSGGOG00000009939	1 retrocopy	retro_ggor_1633,
Macaca mulatta	ENSMMUG00000013307	2 retrocopies	retro_mmul_1695, retro_mmul_985,
Mus musculus	ENSMUSG00000030224	1 retrocopy	retro_mmus_794,
Nomascus leucogenys	ENSNLEG00000004160	2 retrocopies	retro_nleu_1301, retro_nleu_1970,
Ochotona princeps	ENSOPRG00000015211	3 retrocopies	retro_opri_1029, retro_opri_217, retro_opri_541,
Pongo abelii	ENSPPYG00000004334	3 retrocopies	retro_pabe_2005, retro_pabe_3134, retro_pabe_3212,
Pan troglodytes	ENSPTRG00000004734	2 retrocopies	retro_ptro_1538 , retro_ptro_2616,
Tursiops truncatus	ENSTTRG00000003466	2 retrocopies	retro_ttru_581, retro_ttru_974,