RetrogeneDB ID: retro_btau_1688

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:97309642..97310508(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.45558
• Ensembl ID: ENSBTAG00000014417
• Aliases: None
• Description: None

Sequence

>retro_btau_1688
AGGTGCAAGTTCTTCAGTCTGACCAAGACGCCAGAGGATTACACCATCATTGTCGATGAGGAGGGCTTCCTGGAACTGCC
CTCCTCAGAACACCTGGGTGTGCCCGATGCCACCTGGCTGGCCCTCAATGTGGTGTCCAGGGCGGCAGCTTCTCCAGTTT
CCAGCCCACCAGCATGACCAAGATCGTCAAGTCAGTCATCACCCCACTGGCTGATCAGAACATCTCTGTGTCCACGCTGT
CCACCTACCAGATGGACTTCATCCTGGTGCATGAGTAGGACCTGCCCTTCATCACCCACACTTTGTCATCAGAGTTAACC
ACCCTGCACGTCATCAATAGCGAGACGCTGGCAGCTGAGAACCTTGGCATTACACACTGCTTCATGAAGCCCAAGGCGGT
CCAGAGGCCCGTCATCCACCCACTGTCCACCCCAAGCAACAGGTTCTGTGTCACCAGCCTGGACTCTGACATACCGCCCA
CTGTTGCCACACTCCTTATGGACGTCACGTTCTACTCCAGTGGACTGAAGGACCCCCTGGTGTCCTCCGGCGATAACTGT
GGCCACATCCGCTTCTTCTCCTTCTCCCTGATAAAGGGCTACATCTCCCTGGTGAGGGACAAGCAGACCCAGCAGAGGTT
TCCTAGTAATTTGTTGTTCACAAGCGCATCTGGGGGGCTCTGGAAGATGGTGAGGATTGGAGGATAGGCCCCGGGATTTG
ATAAGTGCTTCGAAGTGGCCTGGATCGCTGAGCCTTTGGCTGCCGCAGACATCCAAACCTACTACATCAGCACCTTCAAG
TTCCTCCACACACTGGTGCCGGAAGAAAACATCAGCACCCTGAAAGTCAGCCAAGCAGAAAAATAT

Alignment

ORF - retro_btau_1688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.59 %
• Parental protein coverage: 88.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RCKFFSLTETPEDYTIIVDEEGFLELPSSEHLSVADATWLALNVVSG-GGSFSSSQPIGVTKIAKSVIAP
          RCKFFSLT.TPEDYTIIVDEEGFLELPSSEHL.V.DATWLALNVVS..GGSFSS.QP...TKI.KSVI.P
Retrocopy RCKFFSLTKTPEDYTIIVDEEGFLELPSSEHLGVPDATWLALNVVSR<GGSFSSFQPTSMTKIVKSVITP

Parental  LADQNISVFMLSTYQTDFILVRERDLPFVTHTLSSEFTILRVVNGETVAAENLGITNGFVKPKMVQRPVI
          LADQNISV..LSTYQ.DFILV.E.DLPF.THTLSSE.T.L.V.N.ET.AAENLGIT..F.KPK.VQRPVI
Retrocopy LADQNISVSTLSTYQMDFILVHE*DLPFITHTLSSELTTLHVINSETLAAENLGITHCFMKPKAVQRPVI

Parental  HPLSSPSNRFCVTSLDPDTLPTVATLLMDVMFYSNGVKDPL-ASGDDCDHIRFFSFSLIEGYISLVMDVQ
          HPLS.PSNRFCVTSLD.D..PTVATLLMDV.FYS.G.KDPL..SGD.C.HIRFFSFSLI.GYISLV.D.Q
Retrocopy HPLSTPSNRFCVTSLDSDIPPTVATLLMDVTFYSSGLKDPLVSSGDNCGHIRFFSFSLIKGYISLVRDKQ

Parental  TQQRFPSNLLFTSASGELWKMVRIGGQPLGFDECGIVAQISEPLAAADIPAYYISTFKFDHALVPEENIN
          TQQRFPSNLLFTSASG.LWKMVRIGG...GFD.C..VA.I.EPLAAADI..YYISTFKF.H.LVPEENI.
Retrocopy TQQRFPSNLLFTSASGGLWKMVRIGG*APGFDKCFEVAWIAEPLAAADIQTYYISTFKFLHTLVPEENI-

Parental  GVISALKVSQAEKH
          ...S.LKVSQAEK.
Retrocopy ---STLKVSQAEKY

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	0.22 RPM
ERP005899_muscle	0.00 RPM	13.04 RPM
SRP017611_brain	0.00 RPM	36.22 RPM
SRP017611_kidney	0.00 RPM	23.77 RPM
SRP017611_liver	0.00 RPM	1.21 RPM
SRP030211_testis	0.00 RPM	12.12 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1688 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1688 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014417	1 retrocopy	retro_btau_1688 ,