RetrogeneDB ID: retro_btau_709

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:61931164..61932610(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000030416
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC2A3
• Ensembl ID: ENSBTAG00000004556
• Aliases: None
• Description: solute carrier family 2, facilitated glucose transporter member 3 [Source:RefSeq peptide;Acc:NP_777028]

Sequence

>retro_btau_709
ATGGGGACCGCAAAGGTCACCGCACCTCTGATCTTCACCATCTCAGTTGCTACCATAGGCTCTTTCCAGTTTGGCTACAA
CACTGGAGTCATCAATGCTCCTGAGGAGATCATAAAGGACTTTCTCAATTATGCTTTGGAAAAGTGGTCAGGAACCCCCC
CGTCCAGCATGCTCCTCACATTCCTGTGGTCCTTGTCCGTGGCCATCTTCTCCGTGGGTGGTATGATCGGTTCCTTCTCC
ATCGGACTCTTTGTCAACCGATTTGGCAGGCGCAATTCAATGTTTATTGTCAACCTGTTGGCCATAGCTGGTGGCTGCCT
TATGGGATTCTGCAAAATGGCAGAGTCGGTTGAAATGCTGATCGTGGGCCGACTGGTTATCGGCCTCTTCTGCGGACTCT
GCACAGGATTCGTGCCAATGTACATTGAAGAGATCTCACCTACTGCCCTGCGGGGCGCCTTTGGTACTCTCAACCAGCTG
GGCATCGTTATTGGAATTCTGGTGGCCCAGATCTTTGGTCTAAAAGTCATCTTGGGGACTAAAGAACTCTGGCCTCTGCT
CCTGGTCTTCACCATCATACCAGCCATCATCCAGTGCGCTGCCCTTCCATTTTGCCCTGAAAGTCCTAGATTCTTGCTCA
TTAACAGAAAGCAGGAGGAGAAGGCAAAGGAGGTCCTCCGGAGATTATGGGGCACCGAGGATGTGGCTCAGGACATCCAG
GAGATGAAGGATGAGAGTGTGCGGATGTCGCGGGAGAAGCAAGTCACAGTGCCAGAGCTCTTCCGTGCCCCCAACTACCG
GAAACCCATCATTGTCTCCATCATGCTCCAGCTCTCCCAGCAGCTCTCTGGGATCAATGCAGTGATCTACTACTCGACAG
GAATCTTCAAAGATGCAGGTGTCCAGGAGCCAGTCTATGCCACTGTCGGCACAGGTGTGGTCAACACCATCTTCACCGTG
CTGTCTTTGTTCTTGGTGGAAAGGGCTGGGAGGAGGACTCTACACCTGATTGGCCTTGGAGGGATGGCTTTTTGTTCCAT
CTTCATTATGATTTCTTTGTTACTAAAGAATGATTATAGCTTGATGAACTGTATCTGTATTGGGGCCATCCTGGTCTTCA
TAGCCTTCTTTGAAATTGGCCCAGGCCCCATTCCCTGGTTTATTGTGGCTGAACTCTTCAGCCAGGGACCCCGCCCGGCT
GCCATGGCAGTGGCTGGTTGTTCCAACTGGACCTCCAACTTTTTGGTTGGACTGACCTTCCCCTTGGCCTCATTCTACTT
AGGCGCCCACGTTTTCATCTTCTTCACCATCTTCCTCATTATCTTCTGGGTCTTCACCTTCTTCAAAGTTCCTGAGACCC
GTGGCAGGACTTTTGAGGAAATTACACAAGTCTTTGAAGGGTAGGTGCAGACAGGAACCCATGGTGAGAAAGGCTCCATC
ATGGAG

Alignment

ORF - retro_btau_709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.38 %
• Parental protein coverage: 97.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGTTKVTAPLIFAISVATIGSFQFGYNTGVINAPEAIIKDFLNYTLEERSEPPPSSVLLTSLWSLSVAIF
          MGT.KVTAPLIF.ISVATIGSFQFGYNTGVINAPE.IIKDFLNY.LE..S..PPSS.LLT.LWSLSVAIF
Retrocopy MGTAKVTAPLIFTISVATIGSFQFGYNTGVINAPEEIIKDFLNYALEKWSGTPPSSMLLTFLWSLSVAIF

Parental  SVGGMIGSFSVGLFVNRFGRRNSMLIVNLLAIAGGCLMGFCKIAESVEMLILGRLIIGLFCGLCTGFVPM
          SVGGMIGSFS.GLFVNRFGRRNSM.IVNLLAIAGGCLMGFCK.AESVEMLI.GRL.IGLFCGLCTGFVPM
Retrocopy SVGGMIGSFSIGLFVNRFGRRNSMFIVNLLAIAGGCLMGFCKMAESVEMLIVGRLVIGLFCGLCTGFVPM

Parental  YIGEISPTALRGAFGTLNQLGIVIGILVAQIFGLKVILGTEDLWPLLLGFTILPAIIQCAALPFCPESPR
          YI.EISPTALRGAFGTLNQLGIVIGILVAQIFGLKVILGT..LWPLLL.FTI.PAIIQCAALPFCPESPR
Retrocopy YIEEISPTALRGAFGTLNQLGIVIGILVAQIFGLKVILGTKELWPLLLVFTIIPAIIQCAALPFCPESPR

Parental  FLLINRKEEEKAKEILQRLWGTEDVAQDIQEMKDESMRMSQEKQVTVLELFRAPNYRQPIIISIMLQLSQ
          FLLINRK.EEKAKE.L.RLWGTEDVAQDIQEMKDES.RMS.EKQVTV.ELFRAPNYR.PII.SIMLQLSQ
Retrocopy FLLINRKQEEKAKEVLRRLWGTEDVAQDIQEMKDESVRMSREKQVTVPELFRAPNYRKPIIVSIMLQLSQ

Parental  QLSGINAVFYYSTGIFKDAGVQEPVYATIGAGVVNTIFTVVSVFLVERAGRRTLHLIGLGGMAFCSILMT
          QLSGINAV.YYSTGIFKDAGVQEPVYAT.G.GVVNTIFTV.S.FLVERAGRRTLHLIGLGGMAFCSI...
Retrocopy QLSGINAVIYYSTGIFKDAGVQEPVYATVGTGVVNTIFTVLSLFLVERAGRRTLHLIGLGGMAFCSIFIM

Parental  ISLLLKDNYSWMSFICIGAILVFVAFFEIGPGPIPWFIVAELFGQGPRPAAMAVAGCSNWTSNFLVGLLF
          ISLLLK..YS.M..ICIGAILVF.AFFEIGPGPIPWFIVAELF.QGPRPAAMAVAGCSNWTSNFLVGL.F
Retrocopy ISLLLKNDYSLMNCICIGAILVFIAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLTF

Parental  PSAAFYLGAYVFIVFTVFLVIFWVFTFFKVPETRGRTFEEITRAFEGQTQTGTRGEKGPIME
          P.A.FYLGA.VFI.FT.FL.IFWVFTFFKVPETRGRTFEEIT..FEG..QTGT.GEKG.IME
Retrocopy PLASFYLGAHVFIFFTIFLIIFWVFTFFKVPETRGRTFEEITQVFEG*VQTGTHGEKGSIME

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
ERP005899_liver	0.00 RPM	4.47 RPM
ERP005899_muscle	0.00 RPM	8.34 RPM
SRP017611_brain	0.00 RPM	56.37 RPM
SRP017611_kidney	0.00 RPM	14.11 RPM
SRP017611_liver	0.00 RPM	2.87 RPM
SRP030211_testis	0.11 RPM	627.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_709 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_709 has 0 orthologous retrocopies within eutheria group .

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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,