RetrogeneDB ID: retro_btau_1713

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:88040353..88041486(-)
• Located in intron of: ENSBTAG00000015076

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.79166
• Ensembl ID: ENSBTAG00000016174
• Aliases: None
• Description: nucleolin [Source:RefSeq peptide;Acc:NP_001193589]

Sequence

>retro_btau_1713
CCTGTCAAAGAAGCACCTGGAAAACAAAAGAAGGAAATGGCCAAACAAAAAGCAGCTCCTGAAGCCAAGAAACAAAAAGT
GGAAGGCACAGAACCAACTACGTCTTTCAATCTCTTTGTTGGAAACCTGAACTTCAATAAATCTGCTCCTGAATTGAAAA
CGGGTATCAGTGATCTTTTTGCTAAAAATGATTTTGCTGTTGTTGATGTCAGAATTGGTGTGTCTAGGAAGTTTGGCTAT
GTGGATTTTGAATCTGCCGAAGACCTGGAAAAAGCCTTGGAACTCACTGATTTAAAAGTCTTTGGCAATGAAATTAAACT
AGAAAAACCAGAGGGAAAAGACAGTAAGAAAGATTGAGATGCAAGAACACTTTTGGCTAAAAATCTGCCTTACAAAGTTA
CTCAGGATGAATTAAAAGAAGTGTTTGAAGATGCTGTGGAAATCAGATTAGTCAGCAAGGATGGAAAAAGTAAAGGGATT
GCTTATATTGAATTTAAGACAGAAGCTGATGCAGAAGAAACCTTGGAAGAAAAGCAGGGAACAGAGATAGATGGGCGATC
CATTTCTCTGTACTACACCGGAGAGAAAGGTCAAAGTCAAGACCATAGAGGTGGAAAGAATAGCACTTGGAGTGGTGAAT
GAAAAACCCTGGTTTTAAGCAACCTCTCCTATAGTGCAACCGAAGAAACTCTTAAGCAAGTATTTGAGAAGGCAACTCAT
ATCAAGGTGCCCCAGAACCAAAATGGCAAATCTAAAGGGTATGCATTTATAGAATTTGCTTCATTTGAAGATGCTAAAGA
AGCTTTAAATTCATGTAATAAAAGGGAAATTGAGGGCAGAGCCATCAGACTGGAGTTGCAAGGACCCAGGGGATCACCTA
ATGCAAGAAGCCAGCCATCCAAAACTCTCTTTGTCAAAGGTCTCTCTGAGGATACCACAGAAGAGACGTTAAAAGAGTCG
TTTGATGGCTGTATTCGAGCAAGGATAGTCACTGACCGGGAGACTGGATCCTCCGAAGGGTTTGGTTTTGTAGACTTCAA
CAGCGAGGAAGATGCCAAAGCTGCCAAGGAGGCCATGGAAGATGGTGAAACTGATGGAAACAAAGTCACTTTGGACTGGC
CAAACCTAAGGGT

Alignment

ORF - retro_btau_1713 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.57 %
• Parental protein coverage: 52.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVKEAPGKRKKEMAKQKAAPEAKKQKVEGTEPTTSFNLFVGNLNFNKSAPELKTGISDLFAKNDLAVVDV
          PVKEAPGK.KKEMAKQKAAPEAKKQKVEGTEPTTSFNLFVGNLNFNKSAPELKTGISDLFAKND.AVVDV
Retrocopy PVKEAPGKQKKEMAKQKAAPEAKKQKVEGTEPTTSFNLFVGNLNFNKSAPELKTGISDLFAKNDFAVVDV

Parental  RIGVSRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKDRDARTLLAKNLPYKVTQDELKE
          RIGVSRKFGYVDFESAEDLEKALELT.LKVFGNEIKLEKP.GKDSKKD.DARTLLAKNLPYKVTQDELKE
Retrocopy RIGVSRKFGYVDFESAEDLEKALELTDLKVFGNEIKLEKPEGKDSKKD*DARTLLAKNLPYKVTQDELKE

Parental  VFEDAVEIRLVSKDGKSKGIAYIEFKTEADAEKTLEEKQGTEIDGRSISLYYTGEKGQSQDHRGGKNSTW
          VFEDAVEIRLVSKDGKSKGIAYIEFKTEADAE.TLEEKQGTEIDGRSISLYYTGEKGQSQDHRGGKNSTW
Retrocopy VFEDAVEIRLVSKDGKSKGIAYIEFKTEADAEETLEEKQGTEIDGRSISLYYTGEKGQSQDHRGGKNSTW

Parental  SGESKTLVLSNLSYSATEETLQEVFEKATHIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR
          SGE.KTLVLSNLSYSATEETL..VFEKATHIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR
Retrocopy SGE*KTLVLSNLSYSATEETLKQVFEKATHIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR

Parental  AIRLELQGPRGSPNARSQPSKTLFVKGLSEDTTEETLKESFDGSIRARIVTDRETGSSKGFGFVDFNSEE
          AIRLELQGPRGSPNARSQPSKTLFVKGLSEDTTEETLKESFDG.IRARIVTDRETGSS.GFGFVDFNSEE
Retrocopy AIRLELQGPRGSPNARSQPSKTLFVKGLSEDTTEETLKESFDGCIRARIVTDRETGSSEGFGFVDFNSEE

Parental  DAKAAKEAMEDGEIDGNKVTLDW-AKPKG
          DAKAAKEAMEDGE.DGNKVTLDW.AKPKG
Retrocopy DAKAAKEAMEDGETDGNKVTLDW<AKPKG

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	60.13 RPM
ERP005899_muscle	0.26 RPM	254.65 RPM
SRP017611_brain	0.23 RPM	165.27 RPM
SRP017611_kidney	0.30 RPM	188.54 RPM
SRP017611_liver	0.00 RPM	151.17 RPM
SRP030211_testis	0.27 RPM	292.84 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1713 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1713 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1713 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	ENSBTAG00000016174	1 retrocopy	retro_btau_1713 ,
Myotis lucifugus	ENSMLUG00000014547	1 retrocopy	retro_mluc_685,
Otolemur garnettii	ENSOGAG00000027852	1 retrocopy	retro_ogar_1417,
Tursiops truncatus	ENSTTRG00000009094	2 retrocopies	retro_ttru_1887, retro_ttru_51,