RetrogeneDB ID: retro_btau_1521

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:12274166..12275384(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIP6
• Ensembl ID: ENSBTAG00000024772
• Aliases: None
• Description: Thyroid receptor-interacting protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q3SX26]

Sequence

>retro_btau_1521
CGAGGGGCCGAGGGGCCTCCCCCGCCCACCGAGCAGCGCTCCAGCCCCACCCCTGGGTCAGTTTTTGCCCCCTCCCATCT
GAGCAGTGTTACCAGACCCCCGGGGGACCGGAGGACCGGGGGCTAGCTTGGCTGGGGTGCCACGGAGCACCCCAGCACTC
GCAGGGCCTCCTCCCAGACAGGGGAGGCTTGCGCCCGGAAGTCTGGATGCTGAGATAGACTCCCTGACCAGCATGCTGGC
TGAGTTGGACGGGGGTCGAGGTCACGCCCGCGGCAGCCTGAACGGCAGGCTTACGAGCCCCCTGAGCCCCCTGCCTACCG
CTCAGGGTCAGGCCCCTTGAGGCCGAATGGAGGGGCGCTTCCTCCCCCGCCGCTCCCAGGGTCCCCCTATGGGGGCCCCA
CTCCGGCCTCCTATGCTACGGCCAGCACCCCCGCCGGCCCTGCCTTCCCTGTGCAAGTCAAAGTGGCACAACCCCTGAGA
GGCTGCGGCCGTCCCAGGCGGGGGGCCTCTCAGGCCTCCGGGCCCTCCCTGGGCCCCCATTTTCCTCTCCCAGGCCGAGG
TGAAGTCTGGGGGGCTGGCTACAGGAGCCACCGCGAGCCAGGGCGGGGGGTTAAGGAGGAGGCCCCGGGGGTCTCCGGCC
CTGCAGGCGAAAGAGGAGGCGGGTATGGGTCCCAGGTCCCTCTGAGCCAGCCTCCCGAGAAGGAGCTTGAAAGGCTGACC
AAGAAGCTGGTGCACGACATGAACCACCCGCCCAGCTGGGAGTACTTCGGCCGCTGTGGTGGCTGCGGAGAAGACGTGGT
CGGGGACGGGGTCGGGGCCGTGGCCCTGGATCGCGTCTTCCACGTGGGCTGCTTTGTGTGTTCTGCGTGCGGGGCCCAGC
TCCGGGGCCAGCATTTCTACGCCGTGGAGAGGAGGGCGTATTGTGAGAGCTGCTATGTGGCCACCCTGGAGAAGTGCTCC
ACGTGCTCCCAGCCCATCCTGGACCAGATTCTGCAGGCTATGGGGAAGGCCTACCACCCGGGCTGCTTCACCTGTGTGGT
GTGACACCGCGGCTTGGACGGCATTCCTTTCACTGTGGATGCCACGAGCCAGATCCACTGCATCGAGGACTTCCACAGGA
AGTTTGCCCCAAGATGCTCAGTATGTGGTGGGGCCATCATGCCTGAGCCAGGTCAGGAGGAGACCCTGCGAATCGTAGCT
CTGGATCTCAGTTTTCAC

Alignment

ORF - retro_btau_1521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.2 %
• Parental protein coverage: 84.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RGASGPPL-AHGAALQPHPRVNFCPLPSEQCYQTPGEPEDRGLAWVGCHGAPQHSQGLPPDRGGLRP-GS
          RGA.GPP..AH.AALQPHP.V.FCPLPSEQCYQTPG.PEDRGLAW.GCHGAPQHSQGL.PDRGGLRP.GS
Retrocopy RGAEGPPP<AHRAALQPHPWVSFCPLPSEQCYQTPGGPEDRGLAWLGCHGAPQHSQGLLPDRGGLRP<GS

Parental  LDAEIDSLTSMLAELDGGRGHA-PRRPDRQAYEPPEPPAYRSGSGPLRPNGGALPPPPLPGSPYGAPTPA
          LDAEIDSLTSMLAELDGGRGHA.PR.P.RQAYEPPEPPAYRSGSGPLRPNGGALPPPPLPGSPYG.PTPA
Retrocopy LDAEIDSLTSMLAELDGGRGHA<PRQPERQAYEPPEPPAYRSGSGPLRPNGGALPPPPLPGSPYGGPTPA

Parental  SYATASTPAGPAFPVQVKVARPVRGCGPPRRGASQASGPSPGPHFPLPGRGEVWGAGYRSHREPGPGVKE
          SYATASTPAGPAFPVQVKVA.P.RGCG.PRRGASQASGPS.GPHFPLPGRGEVWGAGYRSHREPG.GVKE
Retrocopy SYATASTPAGPAFPVQVKVAQPLRGCGRPRRGASQASGPSLGPHFPLPGRGEVWGAGYRSHREPGRGVKE

Parental  EAPGVSGPAGARGGGYGPQVPLSQPPEEELERLTKKLVHDMNHPPSGEYFGRCGGCGEDVVGDGAGVVAL
          EAPGVSGPAG.RGGGYG.QVPLSQPPE.ELERLTKKLVHDMNHPPS.EYFGRCGGCGEDVVGDG.G.VAL
Retrocopy EAPGVSGPAGERGGGYGSQVPLSQPPEKELERLTKKLVHDMNHPPSWEYFGRCGGCGEDVVGDGVGAVAL

Parental  DRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCESCYVATLEKCSTCSQPILDRILRAMGKAYHPGCFTCV
          DRVFHVGCFVCS.C.AQLRGQHFYAVERRAYCESCYVATLEKCSTCSQPILD.IL.AMGKAYHPGCFTCV
Retrocopy DRVFHVGCFVCSACGAQLRGQHFYAVERRAYCESCYVATLEKCSTCSQPILDQILQAMGKAYHPGCFTCV

Parental  VCHRGLDGIPFTVDATSQIHCIEDFHRKFAPRCSVCGGAIMPEPGQEETVRIVALDRSFH
          V.HRGLDGIPFTVDATSQIHCIEDFHRKFAPRCSVCGGAIMPEPGQEET.RIVALD.SFH
Retrocopy V*HRGLDGIPFTVDATSQIHCIEDFHRKFAPRCSVCGGAIMPEPGQEETLRIVALDLSFH

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	0.79 RPM
ERP005899_muscle	0.00 RPM	1.48 RPM
SRP017611_brain	0.00 RPM	4.80 RPM
SRP017611_kidney	0.00 RPM	24.89 RPM
SRP017611_liver	0.00 RPM	1.06 RPM
SRP030211_testis	0.01 RPM	3.55 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_1521 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EE892118	12274170	12274345	99.5	170	1	168

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1521 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1521 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018725	1 retrocopy	retro_btau_1013,
Bos taurus	ENSBTAG00000024772	1 retrocopy	retro_btau_1521 ,
Macaca mulatta	ENSMMUG00000021252	1 retrocopy	retro_mmul_2377,