RetrogeneDB ID: retro_btau_969

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:14972008..14972884(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000025379
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OTUD6B
• Ensembl ID: ENSBTAG00000003481
• Aliases: None
• Description: None

Sequence

>retro_btau_969
ATGGAGGCAGTCTTGACTGAGGAGCTTGATGAAGAGGAACAGCTGGTGAGAAGGCATCGCAAAGAGAAGGAGCTGCAAGC
CAAAATACAGAGTTGGAAGAATGCTGTTCCCAGGAATGACAAAAAGAGGAGGAAGCAACTTACAGAAGATGTTGCTAAGT
TAGAAGCAGAAATGGAACAGAAAGAGAGAGAGGAGCTGGATCAGTTGAAGTTGACTTCTAAAGAGAGTAAAATAGATTCT
GTTGCTGTTAATATTTCAAACTTGGTTCTTGAGAATCAGCCACTTCGGATATCAAAAGCACAAAAGAGACGGGACAAAAA
GGCTGCATTGGAAAAGGAGCGGGAAGAAAGGATAGCTGAAGCTGAAATTGAAAACTTAACCGGAGCTAGACATGTAGAAA
GTGAACAACTTGCTCAAATAGTGGCAGCTAGACAGTTGTAAATTAAACAGATTCCATCTGATGGGCACTGTATGTATAGA
GCCATTGAAGATCAGCTGAAAGAGCAGAACGGCGTTTTGACTGTGGCTGCCTTAAGATGTCAGACTGCTAACTATATGCA
GAGTCATGTGGAAGACTTTCTGCCATTTTTAACAAATCCTAATACAGGAGAAATGTATACTCCAGAAGAGTTTGGAAAGT
ATTGTGACGATATTGTAAACACAGCTGCTTGGGGGGGTCAACTTGAGCTAAGAGCCCTGTCTCACATTTTACAAACACCA
ATAGAGATAATACAGGCAGATTCTCCTCCTATAGTAGTTGGTGAAGAATATCCAGAAGATCCATTAATACTTGTTTATAT
GAGACATGCATATGGCTTAGGAGAACACTACAATTCTGTTACACGGTTGGTGAACACAGCTACTGAAAATTGCAGC

Alignment

ORF - retro_btau_969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.27 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAVLTEELDEEEQLVRRHRKEKKELQAKIQSMKNAVPRNDKKRRKQLTEDVAKLEAEMEQKHREELDQL
          MEAVLTEELDEEEQLVRRHRKEK.ELQAKIQS.KNAVPRNDKKRRKQLTEDVAKLEAEMEQK.REELDQL
Retrocopy MEAVLTEELDEEEQLVRRHRKEK-ELQAKIQSWKNAVPRNDKKRRKQLTEDVAKLEAEMEQKEREELDQL

Parental  KLTSKESKIDSVAVNISNLVLENQPLRISKAQKRRDKKAALEKEREERIAEAEIENLTGARHVESEKLAQ
          KLTSKESKIDSVAVNISNLVLENQPLRISKAQKRRDKKAALEKEREERIAEAEIENLTGARHVESE.LAQ
Retrocopy KLTSKESKIDSVAVNISNLVLENQPLRISKAQKRRDKKAALEKEREERIAEAEIENLTGARHVESEQLAQ

Parental  ILAARQLEIKQIPSDGHCMYRAIEDQLKEQNGVLTVAALRCQTANYMQSHVEDFLPFLTNPNTGEMYTPE
          I.AARQL.IKQIPSDGHCMYRAIEDQLKEQNGVLTVAALRCQTANYMQSHVEDFLPFLTNPNTGEMYTPE
Retrocopy IVAARQL*IKQIPSDGHCMYRAIEDQLKEQNGVLTVAALRCQTANYMQSHVEDFLPFLTNPNTGEMYTPE

Parental  EFGKYCDDIVNTAAWGGQLELRALSHILRTPIEIIQADSPPIVVGEEYPENPLILVYMRHAYGLGEHYNS
          EFGKYCDDIVNTAAWGGQLELRALSHIL.TPIEIIQADSPPIVVGEEYPE.PLILVYMRHAYGLGEHYNS
Retrocopy EFGKYCDDIVNTAAWGGQLELRALSHILQTPIEIIQADSPPIVVGEEYPEDPLILVYMRHAYGLGEHYNS

Parental  VTRLVNTATENCS
          VTRLVNTATENCS
Retrocopy VTRLVNTATENCS

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	14.85 RPM
ERP005899_muscle	0.00 RPM	14.89 RPM
SRP017611_brain	0.05 RPM	16.63 RPM
SRP017611_kidney	0.06 RPM	12.86 RPM
SRP017611_liver	0.00 RPM	13.59 RPM
SRP030211_testis	0.64 RPM	9.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_969 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_969 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006971	1 retrocopy	retro_amel_74,
Bos taurus	ENSBTAG00000003481	2 retrocopies	retro_btau_236, retro_btau_969 ,
Choloepus hoffmanni	ENSCHOG00000004266	2 retrocopies	retro_chof_1969, retro_chof_2069,
Cavia porcellus	ENSCPOG00000013595	1 retrocopy	retro_cpor_103,
Equus caballus	ENSECAG00000018205	1 retrocopy	retro_ecab_44,
Felis catus	ENSFCAG00000029900	1 retrocopy	retro_fcat_124,
Loxodonta africana	ENSLAFG00000011002	1 retrocopy	retro_lafr_16,
Microcebus murinus	ENSMICG00000012278	1 retrocopy	retro_mmur_1222,
Myotis lucifugus	ENSMLUG00000016954	1 retrocopy	retro_mluc_1226,
Macaca mulatta	ENSMMUG00000013396	1 retrocopy	retro_mmul_350,
Monodelphis domestica	ENSMODG00000007551	2 retrocopies	retro_mdom_119, retro_mdom_1326,
Mustela putorius furo	ENSMPUG00000009194	1 retrocopy	retro_mputfur_51,
Mus musculus	ENSMUSG00000040550	1 retrocopy	retro_mmus_2456,
Nomascus leucogenys	ENSNLEG00000002420	1 retrocopy	retro_nleu_2365,
Oryctolagus cuniculus	ENSOCUG00000000218	1 retrocopy	retro_ocun_29,
Otolemur garnettii	ENSOGAG00000011298	1 retrocopy	retro_ogar_228,
Ochotona princeps	ENSOPRG00000007655	1 retrocopy	retro_opri_413,
Pan troglodytes	ENSPTRG00000020413	1 retrocopy	retro_ptro_3120,
Sus scrofa	ENSSSCG00000006120	1 retrocopy	retro_sscr_52,
Ictidomys tridecemlineatus	ENSSTOG00000002954	1 retrocopy	retro_itri_9,
Tupaia belangeri	ENSTBEG00000017070	1 retrocopy	retro_tbel_304,
Tursiops truncatus	ENSTTRG00000004345	1 retrocopy	retro_ttru_1207,