RetrogeneDB ID: retro_btau_708

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:61861878..61862721(+)
• Located in intron of: None

Retrocopy information

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

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_708
CTTCCATTTTGCCCTGAAAGTCCTAGATTCTTGCTCATTAACAGAAAGACGATAAAGAAGGCAAAGGAGGTCCTCCAGAG
ATTATGGGGCACTGTAGATGTGGCTCAGGACATCCAGGAGATGCAGAAAGAGAGTGTGCGGATGTCGCGGGAGAAGCAAG
TCACAGTGCTAGAGCTCTTGCGTGCCCCCAACTACCGGAAACGCATCATTGTCTCCATCATGCTCCAGCTCTCCCAGCAG
CTCTCTGGGATCAATGCAGTGATCTACTACTCGACAGGAATCTTCAAAGATGCAGGTGTCCAGGAGCCAGTCCATGCCAC
TATCGGCACAGGTGTGGTCAACACCATCTTCACCGTGCTGTCTTTGTTCTTGGTGGAAAGGGCTGGGAGGAGGACTCTAC
ACCTGATTGGCCTTGGAGGGATGGCTTTTTGTTCCATCTTCATTATGATTTCTTTGTTACTAAAGAATGATTATAGCTGG
ATGGACTGTATCTGTATTGGGGCCATCCTGATCTTCGTGGCCTTCTTTGAAATTGGCCCAGGCCCCATTCCCTGGTTTAT
TGTGGCTGAACTCTTCAGCCAGGGACCCCGCCCGGCTGCCATGGCAGTGGCTGGTTGTTTCAACTGGACCTTCAACTTTT
TGGTTGGACTACTCTTCCCCTTGGCCGCATTCTACTTAGGCGGCCACGTTTTCATCTTCTTCACCATCTTCCTCATTATC
TTCTGGGTCTTCACCTTCTTCAAAGTTCCTGAGACCCGTGGCAGGACTTTTGAGGAAATTACACAAGCCTTTGAAGGGTA
AGTGCAGACAGGAACCCGTGGTGAGAAAGGCCCCATCATGGAG

Alignment

ORF - retro_btau_708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.48 %
• Parental protein coverage: 56.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPFCPESPRFLLINRKEEEKAKEILQRLWGTEDVAQDIQEMKDESMRMSQEKQVTVLELFRAPNYRQPII
          LPFCPESPRFLLINRK...KAKE.LQRLWGT.DVAQDIQEM..ES.RMS.EKQVTVLEL.RAPNYR..II
Retrocopy LPFCPESPRFLLINRKTIKKAKEVLQRLWGTVDVAQDIQEMQKESVRMSREKQVTVLELLRAPNYRKRII

Parental  ISIMLQLSQQLSGINAVFYYSTGIFKDAGVQEPVYATIGAGVVNTIFTVVSVFLVERAGRRTLHLIGLGG
          .SIMLQLSQQLSGINAV.YYSTGIFKDAGVQEPV.ATIG.GVVNTIFTV.S.FLVERAGRRTLHLIGLGG
Retrocopy VSIMLQLSQQLSGINAVIYYSTGIFKDAGVQEPVHATIGTGVVNTIFTVLSLFLVERAGRRTLHLIGLGG

Parental  MAFCSILMTISLLLKDNYSWMSFICIGAILVFVAFFEIGPGPIPWFIVAELFGQGPRPAAMAVAGCSNWT
          MAFCSI...ISLLLK..YSWM..ICIGAIL.FVAFFEIGPGPIPWFIVAELF.QGPRPAAMAVAGC.NWT
Retrocopy MAFCSIFIMISLLLKNDYSWMDCICIGAILIFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCFNWT

Parental  SNFLVGLLFPSAAFYLGAYVFIVFTVFLVIFWVFTFFKVPETRGRTFEEITRAFEGQTQTGTRGEKGPIM
          .NFLVGLLFP.AAFYLG..VFI.FT.FL.IFWVFTFFKVPETRGRTFEEIT.AFEG..QTGTRGEKGPIM
Retrocopy FNFLVGLLFPLAAFYLGGHVFIFFTIFLIIFWVFTFFKVPETRGRTFEEITQAFEG*VQTGTRGEKGPIM

Parental  E
          E
Retrocopy E

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	0.00 RPM	627.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_708 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_708 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,