RetrogeneDB ID: retro_btau_683

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:56084032..56084726(-)
• Located in intron of: ENSBTAG00000003092

Retrocopy information

• Ensembl ID: ENSBTAG00000048014
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.53698
• Ensembl ID: ENSBTAG00000007253
• Aliases: None
• Description: tetraspanin-33 [Source:RefSeq peptide;Acc:NP_001029844]

Sequence

>retro_btau_683
GAGGCAGCGCTGGCCTGCCTGGCCGTGGACCCGGCCATCCTGCTAATCCTGGTGGGCATCCTCAGGTTCCTGCTCACCTT
CTGCAGCTGCATCAGATGATCTCTCTGCGAGAACGTCTGCCTCCTGCAGACGCTCTCCCTCTGTCCCACCATTGTGTTCC
TGCTACAGCTGGCAGCTGGGGTCCTGGGCTTCGTCTTCTCAGACAAGGTGCGGGGCAAAGTGAGTGAGATTATCAATAAT
GCCATTGTGCACTACCGAGATAACTTGGACCTTCAGAATCTCATAGATTTTTGGCCAGAAGGAGTTCAGCTACTGTGGAG
GGATTTCCTATAAGGACTGGTCCCTGAACATGTACTTCAACTGTTCAGAAGACAACCCCAGGCATGAGCACTATTCTGTG
CATTACTCCTGTTGCTTGCCTACCCCTAACCAGGCAGTGATCAACACCATGTGTGGCCAAGGTATGCAGACCTTTGACTA
CTCGGAAGCTAGTCAAGTCATCTACACCCATGGCTGTATTGACAGATTGGTCAACTGGATACACAGCAACCTCTTCATAC
TTGGTGGTGTGGCACTGGGCCTGGCCATCCCGCAGCTCGTGAGAATCCTGCTGTCCATGAACCTTGTGAGTCAGATCAAA
GATCAGATCCAACTATAGCTCTACAACCAGCAGCACCGGGCGGACCCATGGTAC

Alignment

ORF - retro_btau_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.93 %
• Parental protein coverage: 81.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EAALACLAVDPAILLIVVGILMFLLTFCGCIG-SLRENICLLQTFSLCLTVVFLLQLAAGVLGFVFSDKV
          EAALACLAVDPAILLI.VGIL.FLLTFC.CI..SL.EN.CLLQT.SLC.T.VFLLQLAAGVLGFVFSDKV
Retrocopy EAALACLAVDPAILLILVGILRFLLTFCSCIR*SLCENVCLLQTLSLCPTIVFLLQLAAGVLGFVFSDKV

Parental  RGKVSEIINNAIVHYRDDLDLQNLIDF-GQKEFSCCGGISYKDWSLNMYFNCSEDNPSRERCSVPYSCCL
          RGKVSEIINNAIVHYRD.LDLQNLIDF.GQKEFS.CGGISYKDWSLNMYFNCSEDNP..E..SV.YSCCL
Retrocopy RGKVSEIINNAIVHYRDNLDLQNLIDF>GQKEFSYCGGISYKDWSLNMYFNCSEDNPRHEHYSVHYSCCL

Parental  PTPNQAVINTMCGQGMQALDYLEASKVIYTNGCIDRLVNWIHSNLFVLGGVALGLAIPQLVGILLSMILV
          PTPNQAVINTMCGQGMQ..DY.EAS.VIYT.GCIDRLVNWIHSNLF.LGGVALGLAIPQLV.ILLSM.LV
Retrocopy PTPNQAVINTMCGQGMQTFDYSEASQVIYTHGCIDRLVNWIHSNLFILGGVALGLAIPQLVRILLSMNLV

Parental  SQIKDQIKLQLYNQQHRADPWY
          SQIKDQI.L.LYNQQHRADPWY
Retrocopy SQIKDQIQL*LYNQQHRADPWY

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	5.70 RPM
ERP005899_muscle	0.00 RPM	6.60 RPM
SRP017611_brain	0.00 RPM	80.12 RPM
SRP017611_kidney	0.00 RPM	132.12 RPM
SRP017611_liver	0.00 RPM	4.23 RPM
SRP030211_testis	0.08 RPM	7.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_683 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_683 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007253	1 retrocopy	retro_btau_683 ,
Dasypus novemcinctus	ENSDNOG00000007532	1 retrocopy	retro_dnov_2141,