RetrogeneDB ID: retro_btau_107

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:54081476..54082526(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000011945
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TAF7L
• Ensembl ID: ENSBTAG00000001979
• Aliases: None
• Description: None

Sequence

>retro_btau_107
ATGAGTAAGAGCAAAGATGATGCTCCTCATGAACTAGAGAGCCAGTTTATCTTACGCCTACCCCCGGAGTATGCCTCTAC
TGTGAGGCGGGCGGTACAGTCTGGCCATGTCAACTTGAAGGACAGACTGTCAATTGAGTTACACCCTGATGGGCGTCATG
GAATTGTCAGAGTGGACCGAGTCCCTTTGGCCGCAAAATTGGTAGACCTGCCGTGTGTTATGGAGAGTTTGAAAACCATT
GATAAAAAAACCTTTTACAAGACAGCTGATGTCTGTCAGATGCTTGTCTCTACAGTTGATGGTGATCTGTATCCTCCTGT
GGAGGAACCAGTTGCTACTGCTGATCCCAAAGCAAGCAAAAAGAAGGATAAGGACAAAGAGAAAAAATTTGTATGGAACC
ATGGAATTACTCTGCCTCTGAAAAATGTGAGAAAGAGAAGATTCCGTAAGACAGCAAAGAAAAAGTATATTGAGTCTCCA
GATGTGGAAAAAGAAGTAAAACGGTTGCTGAGCACAGATGCTGAAGCTGTCAGTACCCGCTGGGAAATAATTGCTGAAGA
TGAGACAAAAGAAACAGAAAATCAAGGCCTTGATATCTCTTCCCCAGGAATGTCTGGGCATAGGCAGGGCCATGACTCCT
TAGAACATGATGAGCTTCGGGAGATATTCAATGACCTCAGCAGCAGCAGTGAAGATGAAGATGAGACACAGCATCAAGAT
GAAGAAGATATAAACATCATAGACACTGAAGAAGATCTGGAAAGGCAGCTACAGGACAAACTAAATGAATCAGATGAACA
GCACCAAGAAAACGAGGGAACCAATCAGCTGGTTATGGGAATTCAGAAACAGATTGATAACATGAAAGGCAAGCTCCAAG
AGACCCAGGACAGAGCAAAGCGACAGGAGGATCTCATCATGAAAGTGGAAAACCTGGCTCTCAAGAACAGATTTCAGGCT
GTGCTGGATGAACTGAAACAGAAGGAAGACCGGGAAAAAGAGCAGCTCAGCTCTTTGCAAGAAGAGCTAGAATCACTCCT
AGAGAAGTGA

Alignment

ORF - retro_btau_107 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.33 %
• Parental protein coverage: 54.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSSQDEPPHELENQFILRLPMEHASTVRKMVHSGSSSMKNKLKIDLFSDTRHAVVEVDNVSLAAKLVDL
          MS.S.D..PHELE.QFILRLP.E.ASTVR..V.SG....K..L.I.L..D.RH..V.VD.V.LAAKLVDL
Retrocopy MSKSKDDAPHELESQFILRLPPEYASTVRRAVQSGHVNLKDRLSIELHPDGRHGIVRVDRVPLAAKLVDL

Parental  PCVIGSLKTLDRKSFYKTADVSQMLVCTADADVQPSPEEPVTSTDPKAIRKAEKQRKKKYTWKHGITPPL
          PCV..SLKT.D.K.FYKTADV.QMLV.T.D.D..P..EEPV...DPKA..K..K...KK..W.HGIT.PL
Retrocopy PCVMESLKTIDKKTFYKTADVCQMLVSTVDGDLYPPVEEPVATADPKASKKKDKDKEKKFVWNHGITLPL

Parental  RNVRKRKFRKTIKKQHIESPEVEKEVKRLLCSDAEAVNARWEVIAEDETKEIESQG
          .NVRKR.FRKT.KK..IESP.VEKEVKRLL..DAEAV..RWE.IAEDETKE.E.QG
Retrocopy KNVRKRRFRKTAKKKYIESPDVEKEVKRLLSTDAEAVSTRWEIIAEDETKETENQG

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	34.61 RPM	0.29 RPM
ERP005899_muscle	24.07 RPM	0.05 RPM
SRP017611_brain	40.11 RPM	0.41 RPM
SRP017611_kidney	41.02 RPM	0.24 RPM
SRP017611_liver	11.93 RPM	0.15 RPM
SRP030211_testis	21.49 RPM	25.91 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_107 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_107 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009247	1 retrocopy	retro_amel_6,
Bos taurus	ENSBTAG00000001979	1 retrocopy	retro_btau_107 ,
Loxodonta africana	ENSLAFG00000006941	1 retrocopy	retro_lafr_209,
Mus musculus	ENSMUSG00000009596	1 retrocopy	retro_mmus_72,
Oryctolagus cuniculus	ENSOCUG00000004497	1 retrocopy	retro_ocun_191,
Rattus norvegicus	ENSRNOG00000026315	1 retrocopy	retro_rnor_134,