RetrogeneDB ID: retro_pabe_3274

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:89579203..89580264(+)
• Located in intron of: ENSPPYG00000018725

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC2A3
• Ensembl ID: ENSPPYG00000004234
• Aliases: None
• Description: None

Sequence

>retro_pabe_3274
ATAGGGACACAGAAGGTCACTCCAGCTCTGATCGTTGCCATCACAGTTGCTACAATTGGCTCTTTCCAATTTGGCTACAA
CACTGAGGTCATCAATGCTCCTGAGATGATCATAAAGGAATTTATCAATAACACTTTGAGTGACTAGGCAAATATCCCTC
CCTCTGAGATGTTGCTCACGTCCCTCTGGTCCTTGTCTGTGGCCATATTCTCCACTGTTGGTATGACTGGCTCCTTTTCC
GTTAGACTCTTTATCAACCACTTTTGACAGGTACAATTCAATGCTTATCATCAACCTGTTGGCTGTCTCTGGTGGCTGCC
TTATGGGATTGTGTAAAGTGGCTGAGTTGGTTGAAATGCTAATCCTGGGCTGCTTGGTTACTGGCCTCTTCTGTGGACTG
TGCACAGGTTTTATGTCCACGTACATTGGAGAGATCTCACCTACTGCCCTGCAGGGTACCTTTGGCACTCTCAACCAGCT
GGGCATCACTGTTGGAATTCTGGTGGCCCAGATCTTTGGTCTGGAACTCAAATTCATCCTTGGGTCTGAAGAGCTATGGC
CAGTACTATTGGGCTTTACCATCCTTCCTGCTGTCCTACAAAGTGCAGCCCTTCCATTTTGCCCTGAAAGTCCCAGGTTT
TTGCTCATTAACAGAAGAGAAGAGGAGAATGCTAAGTAGATCCTCCAGTGGTTGTGGGGCACCCAGGGTGTATCCCAAGA
CAACCAGGAGATGCAAGATGAGAGTGCAAGGATGTCATAAGAAAAGCAAGTCACCGTGCTGGAGCTCTGTAGCGTATCCA
GCTACCGACAGCCAATCATCATTTCCATCGTGCTCCAGCTCTCTTGACAACTCTCTGGAATCGATGTTGCGTTCTATTAC
TCAACAGGAATCTTCAAGGATGCAGGTGTTCAAGAGCCCATCTATGCCACCATTGGTGCAGGTGTGTTTAATACTATCTT
CATTGTAGTTTCCCTATTTCTGCTAGAAAAGGCAGGAAGAAGGACTCTGCATATGATAGGCCTGGGGAGAGATGGCTTTT
TGTTCCATGCTCATGACTGTT

Alignment

ORF - retro_pabe_3274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.1 %
• Parental protein coverage: 70.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGTQKVTPALIFAITVATIGSFQFGYNTGVINAPETIIKEFIDKSLTDKTNAPPSEVLLTSLWSWSVAIF
          .GTQKVTPALI.AITVATIGSFQFGYNT.VINAPE.IIKEFI...L.D..N.PPSE.LLTSLWS.SVAIF
Retrocopy IGTQKVTPALIVAITVATIGSFQFGYNTEVINAPEMIIKEFINNTLSD*ANIPPSEMLLTSLWSLSVAIF

Parental  SIGGMIGSFSVGLFVNRF-GRRNSMLIVNLLAVTGGCLMGLCKIAKSVEMLILGRLVIGLFCGLCTGFVP
          S..GM.GSFSV.LF.N.F..R.NSMLI.NLLAV.GGCLMGLCK.A..VEMLILG.LV.GLFCGLCTGF..
Retrocopy STVGMTGSFSVRLFINHF>DRYNSMLIINLLAVSGGCLMGLCKVAELVEMLILGCLVTGLFCGLCTGFMS

Parental  MYIGEISPTALRGAFGTLNQLGIVIGILVAQIFGLE--FILGSEELWPVLLGFTILPAILQSAALPCCPE
          .YIGEISPTAL.G.FGTLNQLGI..GILVAQIFGLE..FILGSEELWPVLLGFTILPA.LQSAALP.CPE
Retrocopy TYIGEISPTALQGTFGTLNQLGITVGILVAQIFGLELKFILGSEELWPVLLGFTILPAVLQSAALPFCPE

Parental  SPRFLLINRKEEENAKRILQGLWGTQDVSQDIQEMKDESARMSQEKQVTVLELFRVSSYRQPIIISIVLQ
          SPRFLLINR.EEENAK.ILQ.LWGTQ.VSQD.QEM.DESARMS.EKQVTVLEL..VSSYRQPIIISIVLQ
Retrocopy SPRFLLINRREEENAK*ILQWLWGTQGVSQDNQEMQDESARMS*EKQVTVLELCSVSSYRQPIIISIVLQ

Parental  LSQQLSGINAVFYYSTGIFKDAGVQEPIYATIGAGVVNTVFTVVSLFLVEKAGRRTLHMIGL-GGMAFCS
          LS.QLSGI...FYYSTGIFKDAGVQEPIYATIGAGV.NT.F.VVSLFL.EKAGRRTLHMIGL.G.MAFCS
Retrocopy LS*QLSGIDVAFYYSTGIFKDAGVQEPIYATIGAGVFNTIFIVVSLFLLEKAGRRTLHMIGL>GEMAFCS

Parental  TLMTV
          .LMTV
Retrocopy MLMTV

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	22.17 RPM
SRP007412_cerebellum	0.61 RPM	12.65 RPM
SRP007412_heart	0.15 RPM	7.41 RPM
SRP007412_kidney	0.07 RPM	4.38 RPM
SRP007412_liver	0.03 RPM	15.27 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3274 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3274 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3983
Pan troglodytes	retro_ptro_2703
Macaca mulatta	retro_mmul_2301

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274 ,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703,