RetrogeneDB ID: retro_btau_1682

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:90060046..90060979(+)
• Located in intron of: ENSBTAG00000007159

Retrocopy information

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

Parental gene information

• Parental gene symbol: C5H22orf28
• Ensembl ID: ENSBTAG00000011070
• Aliases: RTCB, C22orf28, C5H22orf28, HSPC117
• Description: tRNA-splicing ligase RtcB homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5E9T9]

Sequence

>retro_btau_1682
ATGAGTTGCTGTTATAATGATGAGCTGCACTTCTTAGAAAAGATCAATAAAAACTGCTAGAGAATCAAGAAGGGCTTCAT
GCCCAACATGCAGGTTGAAGGAGTTTGCTGTGTGAATGATGCTTTGGAAAAATTAATGTTTGAAGAATTAAGGAATGCCT
GTCGAGATGGTGGTGTTGGTACCTTTCTGCCAGCCATGAAACAAATTGGCACTGTGGCTGCCCCGCCTGGTATTGTTCAT
CGATCCATTGGTCTTCCTGATGTCCATTCAGCTTATGGGTTTGCTATTAGGAATAAGGCAGCCTTTAATATGAATGACCC
TGAAGCAGTGGTATCTCCAGATGGTGTTGGATTTGACGTTAACTGTGGTGTCTGCTTGCTGAGAACCAATTTAGACGAAA
GTGATGTTCAGCCTGGGAAGGAGAAACTCGTCTAAGCTATTTTGACCACAGTCCTGTTGGGGTGGGGTCAAAAGGTGTCA
TCCCAATGAATGCCAAAGACTTGGAGGAAGGCTTGGAGATGGGTATAGACTAATTCCTGAGAGAAGGCTATGCCTGGGCG
GAGGACAAGGAGCATTGTGACGAGTACAGAAGGATGCTGCAAGCTGACCCCAATAAAGTCTCAGCGAGGACTAAGAAAAG
AAGCCTTCCCCAGTTGGGGACTCTGGGAGCAGGCAACCACTATGTAGAAATCCAACTTGTTGCTGAGATTTTCAGTGAGT
CTGTTGCTAAGAAAATGAGCATCAGCCATAAGAGACAGATGTGTGTGATGATCAAAAGTGGAAGCAGAAGCTTGGGCCAC
TAAGCCACAGATGCTGTCATAGCTATGGGAAAAGCTATGAAGAGAGAGGATTATAGTCAATGATCATCAGTTGGCTTGTG
CTCGAATTGCTTCCCCAAAGGGTCAGGACTATCTGAAGGCAATGGCAGCAGCT

Alignment

ORF - retro_btau_1682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 61.98 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSRSYNDELQFLEKISKNCWRIKKGFVPNMQVEGVFYVNDSLEKLMFEELRNACRGGGVGGFLPAMKQIG
          MS..YNDEL.FLEKI.KNC.RIKKGF.PNMQVEGV..VND.LEKLMFEELRNACR.GGVG.FLPAMKQIG
Retrocopy MSCCYNDELHFLEKINKNC*RIKKGFMPNMQVEGVCCVNDALEKLMFEELRNACRDGGVGTFLPAMKQIG

Parental  NVAALPGIVHRSIGLPDVHSGYGFAIGNMAAFDMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVK
          .VAA.PGIVHRSIGLPDVHS.YGFAI.N.AAF.MNDPEAVVSP.GVGFD.NCGV.LLRTNLDESDVQP.K
Retrocopy TVAAPPGIVHRSIGLPDVHSAYGFAIRNKAAFNMNDPEAVVSPDGVGFDVNCGVCLLRTNLDESDVQPGK

Parental  EQLAQAM-FDHIPVGVGSKGVIPMNAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRMLQADPNKVSA
          E.L..A..FDH.PVGVGSKGVIPMNAKDLEE.LEMG.D..LREGYAWAEDKEHC.EY.RMLQADPNKVSA
Retrocopy EKLV*AI<FDHSPVGVGSKGVIPMNAKDLEEGLEMGID*FLREGYAWAEDKEHCDEYRRMLQADPNKVSA

Parental  RAKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKGQVCVMIHSGSRGLGHQVATDALVAM-E
          R.KKR.LPQLGTLGAGNHY.EIQ.V.EIF.E..AKKM.I.HK.Q.CVMI.SGSR.LGH..ATDA..AM.E
Retrocopy RTKKRSLPQLGTLGAGNHYVEIQLVAEIFSESVAKKMSISHKRQMCVMIKSGSRSLGH*-ATDAVIAM>E

Parental  KAMKRDKIIVNDRQLACARIASPEGQDYLKGMAAA
          K...R..IIVND.QLACARIASP.GQDYLK.MAAA
Retrocopy K-L*RERIIVNDHQLACARIASPKGQDYLKAMAAA

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	14.64 RPM
ERP005899_muscle	0.00 RPM	48.99 RPM
SRP017611_brain	0.00 RPM	35.81 RPM
SRP017611_kidney	0.00 RPM	47.77 RPM
SRP017611_liver	0.00 RPM	30.81 RPM
SRP030211_testis	0.00 RPM	43.97 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1682 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1682 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011070	1 retrocopy	retro_btau_1682 ,
Canis familiaris	ENSCAFG00000001785	2 retrocopies	retro_cfam_13, retro_cfam_977,
Myotis lucifugus	ENSMLUG00000007803	1 retrocopy	retro_mluc_1461,
Oryctolagus cuniculus	ENSOCUG00000008270	1 retrocopy	retro_ocun_1520,