RetrogeneDB ID: retro_pabe_2442

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:79691896..79692595(+)
• Located in intron of: ENSPPYG00000014861

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX5
• Ensembl ID: ENSPPYG00000010730
• Aliases: None
• Description: sorting nexin 5 [Source:HGNC Symbol;Acc:14969]

Sequence

>retro_pabe_2442
CTAAGTGTTAGGCAGAAAAATACTAAAGAAATGTTTGGTGGCTTCTTCAAAAGTGTGGTGAAAAGTGCTGAAGAAGTCCT
TTTTACTGGAGTTAGGGAGGTAGATGACTTCTTTGAGCAAGAGAAGAACTTCCTTACTAACTATTACAATGGGATCAAAG
ATTCTTGTGTGAAAGCTGACAAAATGACCAGATCTCATAAAAATGTTGCCGATGTCTATATCCACACTGCAGCCTGCTTA
CATAGCCTGGCTTTAGAAGAGCCCACAGTCATCAAAAAGTACCTATTGAAGGTTGCTGTGCTATTTGACAAACTTAGGAA
AGTAGGAGGTCAAGTTTCATCAGATGAAGATCTGAAGCTAACAGAGCTCCTCTGATACTACATGCTCAACATCGAAGCTG
CTAAGGATCTCTTATACAGACACACCAAAGCCCTCATTGATTATGAGAACTTAAACAAAGCTCTGGATAAGGCCTGGTTA
AAGAGCAAAGACGTCAAATTGGCTGAGGCACACCAGCAGGAGTGCTGCCAGAAATTTGAACAGCTTTCCGAATCTGCAAA
AGAAGAACTGATAAATTTCAAACCGAAGAGAGTGGCAGCATTTAGAAAGATTCTCATTGAAATGTCTGAACTGGAAATAA
AACATGCCAGGAACAATGACTCCCTTTTGCAGAGCTGTATTGACTTGTTCAAGAATAAC

Alignment

ORF - retro_pabe_2442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.7 %
• Parental protein coverage: 57.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSVRRKNTKEMFGGFFKSVVKSADEVLFTGVKEVDDFFEQEKNFLINYYNRIKDSCVKADKMTRSHKNVA
          LSVR.KNTKEMFGGFFKSVVKSA.EVLFTGV.EVDDFFEQEKNFL.NYYN.IKDSCVKADKMTRSHKNVA
Retrocopy LSVRQKNTKEMFGGFFKSVVKSAEEVLFTGVREVDDFFEQEKNFLTNYYNGIKDSCVKADKMTRSHKNVA

Parental  DDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEGRVSSDEDLKLTELLRYYMLNIEAAKDLLYR
          D.YIHTAACLHSLALEEPTVIKKYLLKVA.LF.KLRKV.G.VSSDEDLKLTELL.YYMLNIEAAKDLLYR
Retrocopy DVYIHTAACLHSLALEEPTVIKKYLLKVAVLFDKLRKVGGQVSSDEDLKLTELL*YYMLNIEAAKDLLYR

Parental  RTKALIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFEQLSESAKEELINFKRKRVAAFRKNLIEMSE
          .TKALIDYEN.NKALDKA.LKSKDVKLAEAHQQECCQKFEQLSESAKEELINFK.KRVAAFRK.LIEMSE
Retrocopy HTKALIDYENLNKALDKAWLKSKDVKLAEAHQQECCQKFEQLSESAKEELINFKPKRVAAFRKILIEMSE

Parental  LEIKHARNNVSLLQSCIDLFKNN
          LEIKHARNN.SLLQSCIDLFKNN
Retrocopy LEIKHARNNDSLLQSCIDLFKNN

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	20.96 RPM
SRP007412_cerebellum	0.00 RPM	27.60 RPM
SRP007412_heart	0.00 RPM	23.57 RPM
SRP007412_kidney	0.07 RPM	63.97 RPM
SRP007412_liver	0.03 RPM	32.53 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2442 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2442 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2442 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2945
Pan troglodytes	retro_ptro_2052

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 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	ENSPPYG00000005736	2 retrocopies	retro_pabe_1668, retro_pabe_1698,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442 , retro_pabe_877,
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,