RetrogeneDB ID: retro_mmul_2301

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:89080330..89081245(+)
• Located in intron of: ENSMMUG00000006307

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2873
• Ensembl ID: ENSMMUG00000000439
• Aliases: None
• Description: solute carrier family 2, facilitated glucose transporter member 3 [Source:RefSeq peptide;Acc:NP_001248462]

Sequence

>retro_mmul_2301
ATGGGGACACAGAAGGTCACCCCAGCTCTGATCTTCGCCATCACAGTTGCTACAATCGGCTCTTTCCAATTTGGCTATAA
CACTGGGGTCATCAATGCTCCTGAGATGATAATAAAGGAATTTATCAATAACACTTTGAGGGACCAGGCAAATACCCCTC
CCTCTGAGACGCTGCTCATGTCCCTCTGGTCTTTGTCTGTGGCCATATTCTCCATTGTTGGTATGACTGGCTCCTTTTCC
ATTTGACTCTTTGTCAACCACTTTCACAGATGCAATTCAATGCTTATCGTCAACCTGTTGACTGTCTCTGGTGGCTGCCT
TATGGGATTGTGTAAAGTAGCTGAGTTGGTTGAAATGCTGATCCTGGGCTGCTTGGTTATTGGCCTCTTCTGCGGACTGT
GCACAGGTTTTGTACCCATGTACATTGAAGAGATCTCACCTATTGCCCTGCAGGGTACCTTTGGCACTCTCAACCAGCTG
GGCATCATTGTCGGAATTCTAGTGGCCCAAATCTTTGGTCTGGAATTCATCCTTGGGTCTGAAGAGCTATGGCTGGTGCT
ATTGGGCTTTCCCATCCTTCCTGCTATCCTACAAAGTACAGCCCTTCCATTTTGCCCTGAAAGTCCCAGGTTTTTGCTCA
TTAACAGAAAAGAAGAGGAGAATGCTAAGCAGATCCTCCAGCCATTGTGGAGTATCCAGGATGTATCCCAAGACATCCAG
GAGATGCAAGATGAGAGTGCAAGGATGTCACAAGGAAAGCAAGTAACCGTGCTAGAGCTCTTTAGAGTATCCAGCTACCG
AGACCCAATCATCATTTCACTTGTGCTCCAGCTCTCTCGGCAGCTCTCTGGAATCAATGCTGTGTTCTATTACTCAACAG
GAATCTTCAAGGATGCAGGTGTTCAAGAGATCATC

Alignment

ORF - retro_mmul_2301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 61.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGTQKVTPALIFAITVATIGSFQFGYNTGVINAPEKIIKEFINKSLTEKANIPPSEVLLTSLWSLSVAIF
          MGTQKVTPALIFAITVATIGSFQFGYNTGVINAPE.IIKEFIN..L...AN.PPSE.LL.SLWSLSVAIF
Retrocopy MGTQKVTPALIFAITVATIGSFQFGYNTGVINAPEMIIKEFINNTLRDQANTPPSETLLMSLWSLSVAIF

Parental  SVGGMIGSFSVGLFVNRFGRRNSMLIVNLLAVTGGCLMGLCKVAKSVEMLILGRLVIGLFCGLCTGFVPM
          S..GM.GSFS..LFVN.F.R.NSMLIVNLL.V.GGCLMGLCKVA..VEMLILG.LVIGLFCGLCTGFVPM
Retrocopy SIVGMTGSFSI*LFVNHFHRCNSMLIVNLLTVSGGCLMGLCKVAELVEMLILGCLVIGLFCGLCTGFVPM

Parental  YIGEISPTALRGAFGTLNQLGIVIGILVAQIFGLEFILGSEELWPLLLGFTILPAILQSATLPFCPESPR
          YI.EISP.AL.G.FGTLNQLGI..GILVAQIFGLEFILGSEELW..LLGF.ILPAILQS..LPFCPESPR
Retrocopy YIEEISPIALQGTFGTLNQLGIIVGILVAQIFGLEFILGSEELWLVLLGFPILPAILQSTALPFCPESPR

Parental  FLLINRKEEENAKQILQRLWGTQDVSQDIQEMKDESARMSQEKQVTVLELFRVSSYRQPIIISIVLQLSQ
          FLLINRKEEENAKQILQ.LW..QDVSQDIQEM.DESARMSQ.KQVTVLELFRVSSYR.PIIIS.VLQLS.
Retrocopy FLLINRKEEENAKQILQPLWSIQDVSQDIQEMQDESARMSQGKQVTVLELFRVSSYRDPIIISLVLQLSR

Parental  QLSGINAVFYYSTGIFKDAGVQEPI
          QLSGINAVFYYSTGIFKDAGVQE.I
Retrocopy QLSGINAVFYYSTGIFKDAGVQEII

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	0.00 RPM	51.32 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	70.21 RPM
SRP007412_cerebellum	0.65 RPM	51.60 RPM
SRP007412_heart	0.47 RPM	18.25 RPM
SRP007412_kidney	0.12 RPM	6.57 RPM
SRP007412_liver	0.08 RPM	4.12 RPM
SRP007412_testis	0.04 RPM	464.08 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2301 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2301 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3983
Pan troglodytes	retro_ptro_2703
Pongo abelii	retro_pabe_3274

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 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,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
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,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,