RetrogeneDB ID: retro_btau_1742

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:53156011..53156302(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMAGP
• Ensembl ID: ENSBTAG00000001983
• Aliases: None
• Description: Small cell adhesion glycoprotein [Source:UniProtKB/Swiss-Prot;Acc:A4IFL2]

Sequence

>retro_btau_1742
ATGACTAGCCTCCCAACCATGCCTCCTCCAGAACAAGAACTGTTGGCTACCACAATTATACAGGCCACTGAGGCCCTGTC
CCTGATAACTGAAGCCAGCACAGCCCTCATTGTAGTTGTTATCACCGTGGTCTTCCTCACTGTGCTCTCAGTCATGATTT
TGATCTTCTTTTACCTGTAGAAGAACAAAGACAGCTACGTCACTTACGAACCTGCAGATGACAAGCCCAGCGCCATTGTT
CTAATGGAGAATGACTCAGCAAAGGGCAGGGAGAAGGAAGAATATTTCATC

Alignment

ORF - retro_btau_1742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSFPTTPPPAEELMATTILQATEALSPEAEASTALIAVVITVVFLTLLSVVILIFFYLYKNKGSYVTYE
          MTS.PT.PPP..EL.ATTI.QATEALS...EASTALI.VVITVVFLT.LSV.ILIFFYL.KNK.SYVTYE
Retrocopy MTSLPTMPPPEQELLATTIIQATEALSLITEASTALIVVVITVVFLTVLSVMILIFFYL*KNKDSYVTYE

Parental  PADGEPGAVVLMENDSAKGREKEEYFI
          PAD..P.A.VLMENDSAKGREKEEYFI
Retrocopy PADDKPSAIVLMENDSAKGREKEEYFI

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	0.65 RPM
ERP005899_muscle	0.00 RPM	7.44 RPM
SRP017611_brain	0.00 RPM	3.84 RPM
SRP017611_kidney	0.00 RPM	18.49 RPM
SRP017611_liver	0.00 RPM	0.68 RPM
SRP030211_testis	0.00 RPM	18.83 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1742 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1742 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001983	1 retrocopy	retro_btau_1742 ,
Callithrix jacchus	ENSCJAG00000017680	1 retrocopy	retro_cjac_3252,
Dasypus novemcinctus	ENSDNOG00000024893	1 retrocopy	retro_dnov_676,
Mus musculus	ENSMUSG00000053559	2 retrocopies	retro_mmus_2330, retro_mmus_3329,