RetrogeneDB ID: retro_btau_361

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:2068215..2068664(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GBAS
• Ensembl ID: ENSBTAG00000031598
• Aliases: None
• Description: protein NipSnap homolog 2 [Source:RefSeq peptide;Acc:NP_001070479]

Sequence

>retro_btau_361
AGCGGCCTTCCTGGGCGGGCCAGCCCCTGCCGCCTCCTGCCCCATCTCCGGAAACTGACATCTCCCAATAACAGACCTCG
AGAGGACGGCTGGCTAAAATCCTTGTTTGTCCAGAAAGTTGACCCAAGGACAGATGCTCACTCTAACCTCCTAGCCAAAA
AGGAAACCAGCAGTCTGTACAAATTACAGTTTCACAATGTGACACCGGAACGCCTAGAAGCATACAACAAAATCGGTCAA
GAGATGTTGCCACAGATTCATGAAGATAAACATTACCCTTGTACTTTGGTGGGGACTTGGAACACGTGGTATTGCGAGCA
GGATCAAGCTGTTCGCCTCAGGAGATATGAAGGAGGCTATCCAGCTCTCACCGAGGTGATGAATAAACTTAAAGAAAATC
AGGAATTTTGGAATTCCATAAGGCAAGAAGCAACAGGCTTCTCTCGAGA

Alignment

ORF - retro_btau_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.11 %
• Parental protein coverage: 52.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGFLRRASPGSLLPGLRKLTSSDNRPREDSWLKSLFVRKVDPRKDAHSNLLAKKETSSLYKLQFHNVKPE
          SG...RASP..LLP.LRKLTS..NRPRED.WLKSLFV.KVDPR.DAHSNLLAKKETSSLYKLQFHNV.PE
Retrocopy SGLPGRASPCRLLPHLRKLTSPNNRPREDGWLKSLFVQKVDPRTDAHSNLLAKKETSSLYKLQFHNVTPE

Parental  CLEAYNKICQEVLPRIHEDKHYPCTLVGTWNTWYGEQDQAVHLWRYEGGYPALTEVMSKLKENQEF-SEF
          .LEAYNKI.QE.LP.IHEDKHYPCTLVGTWNTWY.EQDQAV.L.RYEGGYPALTEVM.KLKENQEF..EF
Retrocopy RLEAYNKIGQEMLPQIHEDKHYPCTLVGTWNTWYCEQDQAVRLRRYEGGYPALTEVMNKLKENQEF<LEF

Parental  RKARSNMLLSR
          .KARSN.LLSR
Retrocopy HKARSNRLLSR

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	55.30 RPM
ERP005899_muscle	0.00 RPM	39.38 RPM
SRP017611_brain	0.00 RPM	35.86 RPM
SRP017611_kidney	0.00 RPM	129.27 RPM
SRP017611_liver	0.00 RPM	19.78 RPM
SRP030211_testis	0.00 RPM	45.61 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_361 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_361 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_361 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031598	1 retrocopy	retro_btau_361 ,
Macropus eugenii	ENSMEUG00000005152	2 retrocopies	retro_meug_1273, retro_meug_469,
Myotis lucifugus	ENSMLUG00000015038	1 retrocopy	retro_mluc_762,
Oryctolagus cuniculus	ENSOCUG00000001768	1 retrocopy	retro_ocun_1396,
Sarcophilus harrisii	ENSSHAG00000009627	1 retrocopy	retro_shar_473,
Tursiops truncatus	ENSTTRG00000015145	1 retrocopy	retro_ttru_1885,