RetrogeneDB ID: retro_btau_1323

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:67055103..67055801(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD1
• Ensembl ID: ENSBTAG00000009263
• Aliases: None
• Description: Major facilitator superfamily domain-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q1JQC1]

Sequence

>retro_btau_1323
CCTGCTCCCCCCCGGGTGCTGCCGGCCCTCGGCGTCCCCATTGGCCTGGCGCCCTGGCTCTCGGTGCTGTTTCTGATGCA
TGTTTTCAGCAGCATTTTTGGCTGTGATGATCCTGCTGCCCTTCAGACTCAGGTTAAATGGAATATGCGGGTGAGCACCA
CAAAGTTCATGCTACTGTATGCCTGGTATTACTGACCCAACGTAGCTTTGTGTTTCTTTCGTGACTTTTTGATCCACTGA
GTATTTGGAATATGATAGGGAGCCATTATTTTTAGTCGCTTTATTTGCATTGAGCAGGTTATTTTGCTCTGGGTGGACTA
TTTAATGCTTTTTGGCTGATGGAGTTTGGAAAGTTTGCGTTTGGGACTGGTGAGGAGTCCTTAGCACTTGCTCAGAATAC
ATATGCTGTGAATTGGTTTAAAGGCAGAGAATTAAACTCAGTGTTTGGGCTCCAACTTAGCATGGCTAGAAATGGAAGTA
CAGTAACCATAAGCCTCATGGGATGGCCGTATTCTAAGGTTGAAGCTTTGTTGGGTTCTGTTGGTCACACAACACTTGAA
GTCACACTTATGACTGGGGGTATAACATGTATTTTTTCATTAGTTTGTGCCTTGGACTTTGCTTACCTGTATCAGAGAGC
AGAAAGAATTCTTCATGAAGAACAAGGGAAAACAGGTGAGGTTATTCAGTGGCCTGAT

Alignment

ORF - retro_btau_1323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.76 %
• Parental protein coverage: 50.21 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAASGALQALCDPSHLAHRLVVLLLMCFLGFGSYFCYDNPAALQIQVKRDMQVNTTKFMLLYAWYSWPNV
          PA....L.AL..P..LA..L.VL.LM....F.S.F..D.PAALQ.QVK..M.V.TTKFMLLYAWY..PNV
Retrocopy PAPPRVLPALGVPIGLAPWLSVLFLMHV--FSSIFGCDDPAALQTQVKWNMRVSTTKFMLLYAWYY*PNV

Parental  VLCFFGGFLIDRVFGIRWGTIIFSCFVCIGQVV-FALGGIFNAFWLMELGRFVFGIGGESLAVAQNTYAV
          .LCFF..FLI..VFGI..G.IIFS.F.CI.QV..FALGG.FNAFWLME.G.F.FG.G.ESLA.AQNTYAV
Retrocopy ALCFFRDFLIH*VFGI**GAIIFSRFICIEQVI<FALGGLFNAFWLMEFGKFAFGTGEESLALAQNTYAV

Parental  SWFKGKELNLVFGLQLSMARIGSTVNMNLMGWLYSKVEASLGSAGHTTLGVTLMIGGITCILSLVCALAL
          .WFKG.ELN.VFGLQLSMAR.GSTV...LMGW.YSKVEA.LGS.GHTTL.VTLM.GGITCI.SLVCAL..
Retrocopy NWFKGRELNSVFGLQLSMARNGSTVTISLMGWPYSKVEALLGSVGHTTLEVTLMTGGITCIFSLVCALDF

Parental  AYLDQRAERILHKEQGKTGEVIKLTD
          AYL.QRAERILH.EQGKTGEVI...D
Retrocopy AYLYQRAERILHEEQGKTGEVIQWPD

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	131.58 RPM
ERP005899_muscle	0.11 RPM	36.74 RPM
SRP017611_brain	0.05 RPM	26.17 RPM
SRP017611_kidney	0.12 RPM	135.20 RPM
SRP017611_liver	0.00 RPM	70.07 RPM
SRP030211_testis	0.00 RPM	30.63 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1323 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1323 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009263	1 retrocopy	retro_btau_1323 ,
Dasypus novemcinctus	ENSDNOG00000005048	1 retrocopy	retro_dnov_1121,
Macaca mulatta	ENSMMUG00000023510	1 retrocopy	retro_mmul_1210,
Oryctolagus cuniculus	ENSOCUG00000001272	1 retrocopy	retro_ocun_1528,
Pongo abelii	ENSPPYG00000014247	1 retrocopy	retro_pabe_1427,
Tupaia belangeri	ENSTBEG00000013974	1 retrocopy	retro_tbel_1396,
Tursiops truncatus	ENSTTRG00000002207	2 retrocopies	retro_ttru_1119, retro_ttru_1271,
Drosophila melanogaster	FBgn0031636	1 retrocopy	retro_dmel_45,