RetrogeneDB ID: retro_btau_1517

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:8974524..8976192(+)
• 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_1517
GAGAGTGATGGGACTTTCTTGTGAAGCCTGGTGCCCACCCTTCTCCTGATTGGCATCTTCCTCTATGCCATGAGGAGGGG
TCTGATGGGGGCTGGGCATGGTGGGCGAGGAGGGGGCCTCTTTGGCATTGCTGAGACAATAGCCAAGACCATCAAGGATG
ACATCGGTGTGCGGTTTGCAGACGTGGCTGGTTGCGAAGAGGCCAAGCTGGAGATCACGGAGTTTGTGAATTCCCTGAAG
AATTCCAAACAGTACCAGGACCTTGGGGCCAAAATTCCAAAGGGAGCCCTGCTCACAGGTCCTCCTGGTACTGGCAAGAC
GCTTCTCCCCAAGGCAATCATGGGGGAGGCTGGTGTGCCCTTCATCACCATGAATGGGTCTGAGTTCCTGGAGATGTTTG
TTCGTGTTGGCCCAGCTTGGGTTCATGACATGTTTGCAATGGCCTGGAAAAATGCTCCCTGTATCTTGTTTGTTGATGAG
ATTGATGCAATTGGCAGAAGCGTGGCTGCAGGCACTTTGGAGGCCGGAGTGAGCAGAACACCCTGAACCAGCTGCTCGTG
GAGATGGACGGATTCAACTCTACCACGAACGTCATCGTGCTGGCCAGCACCAACCGTCCCCACGTCCTTGACCCAGCCCT
GATGCGGCCGGGCCGCTTCGACCATCAGATTTACACTGGCCCCCCGGACATCAAAGGCAGGTCGTCTATCTTCAGGGTCC
ACCTGCGTCCACTCAAGTTGGACAAGAGCCTCAGCAAGGATGCCCTGGTGAGGAAGCTTGCGGCCCTCACTCCAGGCTTC
ACAGGTGCTGATATTTCTAATGTTTGCAACGAAGCCGCCCTGATTGCCACCCGCCACCTAAACCCCTGTGTCGGGGAGAA
GCACTTCGAGCAGGCCATCCAGAGGGTCATTGGAGGCCTTGAGAAGAAGACACAGGTCCTGCAGCCCTGCGAGAAGATGA
TGGTGGCCTACCACGAGGCTGGCCGTGAGGTGGTGGGCTGGTTCCTGGAACATGCAGACTCCCTGCTCAAGGTGTCCATT
GTCCCCCGGGGCAAGGGGCTCAGCTATGCCCAGTGCCTGCCCAGGGAGTAGTACCTGTACACACCGGAGCAGCTCTTTGA
CCGCTTGTGTGCCATGTTGGGCAGCCGCATGGCTGAGCAGCTGTTTTTCGGGCGGGTCACCACGGGGGCCCAGGATGACC
TGAGGAAGGTCACCCAGAGCGCCTAGGCTCAGATCATGCAGTTCGGGATGAGCGAGAAGCTGGGCCAGGTGTCCTTCGAC
CTCCCGTGGCCAGGAGAGGCGCTGGTGGAGAAGCCATTCAGCGAGGCCATGGCCCAGTTCATAGACGAGGAGGTGCGGTA
GCTCATCGGCTCCGCGCTTGCATGCACTCTGGACCTGCTTATATGCTACTGTGAGCAGGTGGACAAGGTGGGCAGGCGGC
TGCTGAAGAAGGAGGTGCTGGAGCAGGCTGACATGGTGGAGCTGCTTGGGCCGCGGCTGTTCGCTGAGAAGATCACCTAC
GAGGAGCTCGTGGAGGGCACGGGAGGCCTGGAGGAGGACACGGCCCTTCCCGAGGGTCTGCAGGGCTGGCATGGGGGGCC
TGCTGCAGGAGAGCCCAGCCTGGCGCCTCTGCCTGGAGAGCAGCCTCCGGGACCCCCAGGAAGCAAAT

Alignment

ORF - retro_btau_1517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.06 %
• Parental protein coverage: 69.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESDGTFLRSLVPTLLLIGIFLYAMRRGPMGAGRGGRGGRLFGIGETIAKIIKDDIGVRFADVAGCEEAKL
          ESDGTFL.SLVPTLLLIGIFLYAMRRG.MGAG.GGRGG.LFGI.ETIAK.IKDDIGVRFADVAGCEEAKL
Retrocopy ESDGTFL*SLVPTLLLIGIFLYAMRRGLMGAGHGGRGGGLFGIAETIAKTIKDDIGVRFADVAGCEEAKL

Parental  EIMEFVNFLKNPKQYQDLGAKIPKGALLTGPPGTGKTLLAKATAGEAGVPFITVNGSEFLEMFVGVGPAR
          EI.EFVN.LKN.KQYQDLGAKIPKGALLTGPPGTGKTLL.KA..GEAGVPFIT.NGSEFLEMFV.VGPA.
Retrocopy EITEFVNSLKNSKQYQDLGAKIPKGALLTGPPGTGKTLLPKAIMGEAGVPFITMNGSEFLEMFVRVGPAW

Parental  VRDMFALARKNAPCILFVDEIDAIGR-KRGRGHFGGQSEQENTLNQLLVEMDGFNSTTNVVVLAGTNRPD
          V.DMFA.A.KNAPCILFVDEIDAIGR.KRG..HFGG.SEQ.NTLNQLLVEMDGFNSTTNV.VLA.TNRP.
Retrocopy VHDMFAMAWKNAPCILFVDEIDAIGR<KRGCRHFGGRSEQ-NTLNQLLVEMDGFNSTTNVIVLASTNRPH

Parental  VLDPALMRPGRFDRQIYIGPPDIKGRSSIFRVHLRPLKLDESLSKDALARKLAALTPGFTGSGADISNVC
          VLDPALMRPGRFD.QIY.GPPDIKGRSSIFRVHLRPLKLD.SLSKDAL.RKLAALTPGFTG..ADISNVC
Retrocopy VLDPALMRPGRFDHQIYTGPPDIKGRSSIFRVHLRPLKLDKSLSKDALVRKLAALTPGFTG--ADISNVC

Parental  NEAALIAARHLNPSVGEKHFEQAIERVIGGLEKKTQVLQPGEKMTVAYHEAGHAVVGWFLEHADPLLKVS
          NEAALIA.RHLNP.VGEKHFEQAI.RVIGGLEKKTQVLQP.EKM.VAYHEAG..VVGWFLEHAD.LLKVS
Retrocopy NEAALIATRHLNPCVGEKHFEQAIQRVIGGLEKKTQVLQPCEKMMVAYHEAGREVVGWFLEHADSLLKVS

Parental  IVPRGKGLGYAQCLPREQYLYTREQLFDRMCAMLGGRVAEQLFFGRVTTGAQDDLRKVTQSAYAQIVQFG
          IVPRGKGL.YAQCLPRE.YLYT.EQLFDR.CAMLG.R.AEQLFFGRVTTGAQDDLRKVTQSA.AQI.QFG
Retrocopy IVPRGKGLSYAQCLPRE*YLYTPEQLFDRLCAMLGSRMAEQLFFGRVTTGAQDDLRKVTQSA*AQIMQFG

Parental  MSEKLGQVSFDLPRPGEALVEKPFSEATAQLIDEEVRRLIGSAHARTLDLLTRCREQVDKVGRRLLEKEV
          MSEKLGQVSFDLP.PGEALVEKPFSEA.AQ.IDEEVR.LIGSA.A.TLDLL....EQVDKVGRRLL.KEV
Retrocopy MSEKLGQVSFDLPWPGEALVEKPFSEAMAQFIDEEVR*LIGSALACTLDLLICYCEQVDKVGRRLLKKEV

Parental  LERADMVELLGPRPFAEKVTYEELVEGTGGLEEDTALPEGLQGWRGGPTAGEPSLAPPPGEQPLG-PQEA
          LE.ADMVELLGPR.FAEK.TYEELVEGTGGLEEDTALPEGLQGW.GGP.AGEPSLAP.PGEQP.G.PQEA
Retrocopy LEQADMVELLGPRLFAEKITYEELVEGTGGLEEDTALPEGLQGWHGGPAAGEPSLAPLPGEQPPG>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	0.00 RPM	27.38 RPM
SRP017611_liver	0.00 RPM	5.06 RPM
SRP030211_testis	0.01 RPM	50.35 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1517 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1517 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,