RetrogeneDB ID: retro_ptro_2052

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:53722160..53722854(-)
• Located in intron of: ENSPTRG00000016189

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX5
• Ensembl ID: ENSPTRG00000013278
• Aliases: None
• Description: Sorting nexin 5 [Source:UniProtKB/TrEMBL;Acc:K7BDP9]

Sequence

>retro_ptro_2052
CTAAGTGTTAGGTGGAAAAATACTAAAGAAATGTTTGGTGGCTTCTTCAAAAGTGTGGTGAAAAGTGCTGAAGAAGTCCT
TTTTACTGGAGTTAGGGAGGTAGATGACTTCTTTGAGCAAGAGAAGAACTTACTTACTAACTATTACAATAGGATCAACG
ATTCTTGTGTGAAAGCTGACAAAATGACCAGATCTCATAAAAATTGTTGCCGATGTCTATATCCACACTGCAGCCTGCTT
ACATTGCCTGGCTTTAGAAGAGCCCACAGTCATCAAAAAGTACCTATTGAAGGTTGCTGTGCTATTTGACAAACTTAGGA
AAGTAGAGGGTCAGGTTTCATCAGATGAAGATCTGAAGCTAACAGAGCTCCTCCGATACTACATGCTCAACATCGAAGCT
GCTAAGGATCTCTTATACAGACACACCAAAGCCCTCATTGATTATGAGAACTCAAACAAAGCTCTGGATAAGGCCTGGTT
AAAGAGCAAAGACGTCGAATTGGCTGAGGCACACCAGCAGGAGTGCTGCCCGAAATCTGAACAGCTTTCCAAATCTGCAA
AAGAAGAAGTGATAAATTTCAAACCGAAGAGAGTGGCAGCATTTAGAAAGATTCTCATTGAAATGTCTGAACTGGAAATA
AAACATGCCAGGAACAATGACTCCCTTTTGCAGAGCTGTATTGACTTGTTCAAG

Alignment

ORF - retro_ptro_2052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.52 %
• Parental protein coverage: 57.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSVRRKNTKEMFGGFFKSVVKSADEVLFTGVKEVDDFFEQEKNFLINYYNRIKDSCVKADKMTRSHKN-V
          LSVR.KNTKEMFGGFFKSVVKSA.EVLFTGV.EVDDFFEQEKN.L.NYYNRI.DSCVKADKMTRSHKN.V
Retrocopy LSVRWKNTKEMFGGFFKSVVKSAEEVLFTGVREVDDFFEQEKNLLTNYYNRINDSCVKADKMTRSHKN>V

Parental  ADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEGRVSSDEDLKLTELLRYYMLNIEAAKDLLY
          AD.YIHTAACLH.LALEEPTVIKKYLLKVA.LF.KLRKVEG.VSSDEDLKLTELLRYYMLNIEAAKDLLY
Retrocopy ADVYIHTAACLHCLALEEPTVIKKYLLKVAVLFDKLRKVEGQVSSDEDLKLTELLRYYMLNIEAAKDLLY

Parental  RRTKALIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFEQLSESAKEELINFKRKRVAAFRKNLIEMS
          R.TKALIDYENSNKALDKA.LKSKDV.LAEAHQQECC.K.EQLS.SAKEE.INFK.KRVAAFRK.LIEMS
Retrocopy RHTKALIDYENSNKALDKAWLKSKDVELAEAHQQECCPKSEQLSKSAKEEVINFKPKRVAAFRKILIEMS

Parental  ELEIKHARNNVSLLQSCIDLFK
          ELEIKHARNN.SLLQSCIDLFK
Retrocopy ELEIKHARNNDSLLQSCIDLFK

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	0.23 RPM	12.62 RPM
SRP007412_cerebellum	0.11 RPM	15.41 RPM
SRP007412_heart	0.06 RPM	16.15 RPM
SRP007412_kidney	0.24 RPM	76.81 RPM
SRP007412_liver	0.07 RPM	19.74 RPM
SRP007412_testis	0.21 RPM	19.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2052 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2052 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2052 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2945
Pongo abelii	retro_pabe_2442

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478, retro_chof_2166,
Callithrix jacchus	ENSCJAG00000004947	2 retrocopies	retro_cjac_2192, retro_cjac_3243,
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746, retro_mmul_832,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071,
Oryctolagus cuniculus	ENSOCUG00000017072	1 retrocopy	retro_ocun_1323,
Otolemur garnettii	ENSOGAG00000006157	1 retrocopy	retro_ogar_1203,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000006253	1 retrocopy	retro_ptro_1362,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052 , retro_ptro_717,
Sus scrofa	ENSSSCG00000007088	1 retrocopy	retro_sscr_593,
Ictidomys tridecemlineatus	ENSSTOG00000015416	1 retrocopy	retro_itri_1176,
Tursiops truncatus	ENSTTRG00000016432	1 retrocopy	retro_ttru_410,