RetrogeneDB ID: retro_btau_1055

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 24:59566798..59568042(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.30326
• Ensembl ID: ENSBTAG00000038051
• Aliases: None
• Description: None

Sequence

>retro_btau_1055
AAGCACATTTTTACCCTTCTGTTACTAAATGGAATTTTCATTCTTTTTCTTCTCTGACCCAACAAATTGGCCAGAAGCAT
GGCCGAGGGCACTTTGGAGGCCAGAGTGAGCAGGAGAACACCCTGAACCAGCTGCTCGTGGAGATGGACGGATTCAACTC
TACCACGAACGTCCTCACGCTGGCCGGCACCAACCGCCCTGACGTCCTTGAGCCAGCTCTGATGCGGCCGGGCCGCTTCA
ACCGTCAGATTTACACTGGGCCCCTGGACATCAAAGGCAGGTCGTCTATCTTCAAGGTCCACTTGCGTTCACTCAAGTTG
GACGAGAGCCTCAGCAAGGATGCCCAGGCGAGGAAGCCTGCGGCCCTCACTCCAGGCTTCACAGGTGCTGATATTTCTAA
TGTTTGCAACGAAGCCACCCTGATTGCCGCCCGCCACCTAAACCCGTCTGTCGGGGAGAAGCACTTCGAGCAGGCCATCG
AGAGGGTCATTGGAGGCCTTGAGAAGAAGACACAGGCCTGCAGCCCGGTGAGAAGATGACGGTGGCCTACCATGAGGCTG
GCCATGCGGTGGTGGGCTGGTTCCTGGAACATGCAGACCACCTGCTCAAGGTGTCCATCGTCCCCCAGGGCAAGGGGCTC
GGCTATGCGCAGTGCCTGCCCAGGGAGCAGTACCTGTACACACGGGAGCAGCTCTCTGACTGCATGTGTGCCATGCTGGG
CGGCCGCATGGCTAAGCGGCTGTTCTTCGGGCGGGTCACCACGGGGACCCAGGACGGCTTGAGAAAGGTCACCCAGAGCG
CCTATGCCCAGATTGTGCATTTCGGGATGAGCGAGAAGCTGGGCCAGGTGTCCTTCGATCTCCCGTGGTCAGGCGAGGTG
CTGGTGGAGAAACTGTTCAGTGAGGCCGCGGCCCAGCTTATAGATGAGGAGGTGCGGCGGCCCATTGGCTCCGTGCATGC
GCGCACCCTGGACCTGCTTACTGGCTGCCGCGAGCAGGTGGACAAGGTGGGCAGGGGGCTGCTGGAGAAGGAGGTGTTGG
AGCGGGCCGACATGGTGGAGCTGCTCAAGCCGCGGCCGTTCGCCGAGATCACCTACGAGGAGCTCGTGGAGGGCACGGGC
GGCCTGGAAAAGGACACGGCCCTTCCTGAGGGTCTGCAGGGTTGGCGTGGGGGGCCTGCTTCAGGAGAGCCCAGCCTAGC
GCCTCTGCCTGGAGAGCAGCCTCTGGGACCCCCAGGAAGCAAAT

Alignment

ORF - retro_btau_1055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.51 %
• Parental protein coverage: 52.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RDMFALARKNAPCILFV-DEIDAIGRKRGRGHFGGQSEQENTLNQLLVEMDGFNSTTNVVVLAGTNRPDV
          ...F.L...N...ILF.......IG.K.GRGHFGGQSEQENTLNQLLVEMDGFNSTTNV..LAGTNRPDV
Retrocopy KHIFTLLLLNGIFILFL<SLTQQIGQKHGRGHFGGQSEQENTLNQLLVEMDGFNSTTNVLTLAGTNRPDV

Parental  LDPALMRPGRFDRQIYIGPPDIKGRSSIFRVHLRPLKLDESLSKDALARKLAALTPGFTGSGADISNVCN
          L.PALMRPGRF.RQIY.GP.DIKGRSSIF.VHLR.LKLDESLSKDA.ARK.AALTPGFTG..ADISNVCN
Retrocopy LEPALMRPGRFNRQIYTGPLDIKGRSSIFKVHLRSLKLDESLSKDAQARKPAALTPGFTG--ADISNVCN

Parental  EAALIAARHLNPSVGEKHFEQAIERVIGGLEKKTQV-LQPGEKMTVAYHEAGHAVVGWFLEHADPLLKVS
          EA.LIAARHLNPSVGEKHFEQAIERVIGGLEKKTQ..LQPGEKMTVAYHEAGHAVVGWFLEHAD.LLKVS
Retrocopy EATLIAARHLNPSVGEKHFEQAIERVIGGLEKKTQA<LQPGEKMTVAYHEAGHAVVGWFLEHADHLLKVS

Parental  IVPRGKGLGYAQCLPREQYLYTREQLFDRMCAMLGGRVAEQLFFGRVTTGAQDDLRKVTQSAYAQIVQFG
          IVP.GKGLGYAQCLPREQYLYTREQL.D.MCAMLGGR.A..LFFGRVTTG.QD.LRKVTQSAYAQIV.FG
Retrocopy IVPQGKGLGYAQCLPREQYLYTREQLSDCMCAMLGGRMAKRLFFGRVTTGTQDGLRKVTQSAYAQIVHFG

Parental  MSEKLGQVSFDLPRPGEALVEKPFSEATAQLIDEEVRRLIGSAHARTLDLLTRCREQVDKVGRRLLEKEV
          MSEKLGQVSFDLP..GE.LVEK.FSEA.AQLIDEEVRR.IGS.HARTLDLLT.CREQVDKVGR.LLEKEV
Retrocopy MSEKLGQVSFDLPWSGEVLVEKLFSEAAAQLIDEEVRRPIGSVHARTLDLLTGCREQVDKVGRGLLEKEV

Parental  LERADMVELLGPRPFAEKVTYEELVEGTGGLEEDTALPEGLQGWRGGPTAGEPSLAPPPGEQPLG-PQEA
          LERADMVELL.PRPFAE..TYEELVEGTGGLE.DTALPEGLQGWRGGP..GEPSLAP.PGEQPLG.PQEA
Retrocopy LERADMVELLKPRPFAE-ITYEELVEGTGGLEKDTALPEGLQGWRGGPASGEPSLAPLPGEQPLG>PQEA

Parental  N
          N
Retrocopy N

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	1.15 RPM
ERP005899_muscle	0.00 RPM	16.36 RPM
SRP017611_brain	0.00 RPM	22.11 RPM
SRP017611_kidney	0.24 RPM	27.38 RPM
SRP017611_liver	0.00 RPM	5.06 RPM
SRP030211_testis	0.14 RPM	50.35 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1055 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1055 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011250	1 retrocopy	retro_btau_958,
Bos taurus	ENSBTAG00000038051	2 retrocopies	retro_btau_1055 , retro_btau_1517,
Ornithorhynchus anatinus	ENSOANG00000002348	1 retrocopy	retro_oana_37,