RetrogeneDB ID: retro_btau_1757

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:93524313..93525053(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1D
• Ensembl ID: ENSBTAG00000016309
• Aliases: ATP6V1D, VATD
• Description: V-type proton ATPase subunit D [Source:RefSeq peptide;Acc:NP_001068609]

Sequence

>retro_btau_1757
ATGTCGGGCAAAGACTGAATTGAAATCTTTCCCTCACGAAGGGCACAGACCATCATGAAGGCTCAGTTAAAAGGAGCACA
GACAGGTCGAAACCTCCTGAAGAAAAAATCTGATCCTTAACTCTTTGATTTCGACATATCCTTAAGAAGATAATAGAGAC
TAAAATGTTGATGGGTGAAGTGATGAGAGAGGTTGCTTTTTCACTTGCTGAGGCCAAGTTCACAGCAGGGGACTTCAGCA
CCACAGTTATCCAAAATGTAAATAAGGCCCAAGTGAAGATTAGAGCAAAGAAAGATAATGTAGCAGGTGTGACATTGCCA
GTATTTGAACATTATCATGAAGGAACTGACAATTATGAACTGACTGGTTTAGCCGGAGGTGGGGAACAGTTGGCTAAACT
GAAGAGGAATTATGCCCAAGCAGTGGAACTACTGGTGGAACTGGCTTCTCTGCAGACTTCCTTTGTTACTTTGGATGAAG
CTATTAAGATAACTGACAGGCATGTAAATGCTATAGAACATGTCATCATTCCCCGGATTGAACATACCCTTGCTTATATT
ATCACAGAGCTGGATGAGAGAGAGCAAGAGGAGTTCTACAGGTTAAGGAAAATTCAGGAGAAGAAAAAGATTCTCAAGGA
AAAGTTTGATAAGGACTTGGAGCAACGGAGGGCAGCCAAAGAGATGATAGAGCCTGCTAATCTCCTGGTTGAAAAGAAGG
ATGAAGATTTTCTGTTTGAA

Alignment

ORF - retro_btau_1757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSD-ALTLRFRQILKKIIETKMLMGEVMREAAFSL
          MSGKD.IEIFPSR.AQTIMKA.LKGAQTGRNLLKKKSD..LTL.FR.ILKKIIETKMLMGEVMRE.AFSL
Retrocopy MSGKD*IEIFPSRRAQTIMKAQLKGAQTGRNLLKKKSD<SLTL*FRHILKKIIETKMLMGEVMREVAFSL

Parental  AEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYA
          AEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTD.YELTGLA.GGEQLAKLKRNYA
Retrocopy AEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDNYELTGLAGGGEQLAKLKRNYA

Parental  KAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKK
          .AVELLVELASLQTSFVTLDEAIKIT.R.VNAIEHVIIPRIE.TLAYIITELDERE.EEFYRL.KIQEKK
Retrocopy QAVELLVELASLQTSFVTLDEAIKITDRHVNAIEHVIIPRIEHTLAYIITELDEREQEEFYRLRKIQEKK

Parental  KILKEKSDKDLEQRRAAGEVIEPANLLAEEKDEDLLFE
          KILKEK.DKDLEQRRAA.E.IEPANLL.E.KDED.LFE
Retrocopy KILKEKFDKDLEQRRAAKEMIEPANLLVEKKDEDFLFE

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	44.63 RPM
ERP005899_muscle	0.05 RPM	32.10 RPM
SRP017611_brain	0.14 RPM	72.81 RPM
SRP017611_kidney	0.00 RPM	93.12 RPM
SRP017611_liver	0.00 RPM	22.58 RPM
SRP030211_testis	0.04 RPM	117.31 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1757 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1757 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1757 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008240	1 retrocopy	retro_amel_332,
Bos taurus	ENSBTAG00000016309	2 retrocopies	retro_btau_1757 , retro_btau_408,
Canis familiaris	ENSCAFG00000016369	2 retrocopies	retro_cfam_1186, retro_cfam_999,
Choloepus hoffmanni	ENSCHOG00000003733	5 retrocopies	retro_chof_1229, retro_chof_2711, retro_chof_54, retro_chof_926, retro_chof_938,
Cavia porcellus	ENSCPOG00000009085	1 retrocopy	retro_cpor_36,
Felis catus	ENSFCAG00000011078	1 retrocopy	retro_fcat_632,
Myotis lucifugus	ENSMLUG00000006244	5 retrocopies	retro_mluc_2345, retro_mluc_442, retro_mluc_540, retro_mluc_666, retro_mluc_94,
Macaca mulatta	ENSMMUG00000021418	1 retrocopy	retro_mmul_1159,
Monodelphis domestica	ENSMODG00000009896	5 retrocopies	retro_mdom_1196, retro_mdom_1522, retro_mdom_1730, retro_mdom_390, retro_mdom_594,
Mustela putorius furo	ENSMPUG00000007002	2 retrocopies	retro_mputfur_1381, retro_mputfur_748,
Otolemur garnettii	ENSOGAG00000015052	1 retrocopy	retro_ogar_966,
Sus scrofa	ENSSSCG00000002288	1 retrocopy	retro_sscr_357,
Ictidomys tridecemlineatus	ENSSTOG00000027710	1 retrocopy	retro_itri_383,
Vicugna pacos	ENSVPAG00000005696	1 retrocopy	retro_vpac_232,
Drosophila melanogaster	FBgn0040377	1 retrocopy	retro_dmel_70,