RetrogeneDB ID: retro_btau_1180

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:32860722..32861451(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000024731
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSBTAG00000002108
• Aliases: None
• Description: 14-3-3 protein theta [Source:UniProtKB/Swiss-Prot;Acc:Q3SZI4]

Sequence

>retro_btau_1180
ATGGAGAAGACGGAGCTGATCCAGAAGGTCAAGCTGGCCGAGCAGGCCGAGCACTACGACGACATGGCCACCTGCATGAA
GGCCATGACGGAGCAGGGCGCCGAGCCGTCCAACGAGGAGCGCAACCTGCTGTCGGTGGCCTACAAGGTGGTCGGGGGCC
GCCGGTCCGCCTGGAGGGTCATCTCCAGCTTCGAGCAGAAGACCGACACCTCGGACAAGAAGTTACAGCTGATCAAGGAC
TACTGGGAAAAAGTGGAGTCCAAGCTGAGGTCCATCTGCACCACGGTCCTAGAATTGTTGGATAAGTATTTAACAGCCAA
TGCAACTAATCCAGAGAGTGTCTTCTATCTGAAAATGAAGGGAGATTACTTCCGGTACCTTGCTGAAGTTGCTTGTGATG
ATGATCAGAAGCAAACAATAGATAATTCCCAAGGAGCTTACCAAGAGGCTTTCCATATAAGCAAGAAAGAGATGCAACCC
ACACACCCCATCGGGCTGGGGCTGGCTCTTAACTTTTCTGTGCTCTACTATGAGATCCTCAATAACCCAGAACTGGCCTG
CACACTGGCTAAAACGGCTTTTGATGAGGCTCTTGCAGAACTCGACACACTGAATGAAGACTCATGCAAAGACAGCACCC
TCATCATGCAGCTGCTGAGAGACAACCTCGCATTATGGACATCAGACAGTGCAGGAGAAGAACGTGATGTGGCAGAAGGG
GCAGAAAAC

Alignment

ORF - retro_btau_1180 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKTELIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTD
          MEKTELIQK.KLAEQAE.YDDMATCMKA.TEQGAE.SNEERNLLSVAYK.VVGGRRSAWRVISS.EQKTD
Retrocopy MEKTELIQKVKLAEQAEHYDDMATCMKAMTEQGAEPSNEERNLLSVAYK-VVGGRRSAWRVISSFEQKTD

Parental  TSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQ
          TSDKKLQLIKDY.EKVES.LRSICTTVLELLDKYL.ANATNPES.VFYLKMKGDYFRYLAEVAC.DD.KQ
Retrocopy TSDKKLQLIKDYWEKVESKLRSICTTVLELLDKYLTANATNPES-VFYLKMKGDYFRYLAEVACDDDQKQ

Parental  TIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDS
          TIDNSQGAYQEAF.ISKKEMQPTHPI.LGLALNFSV.YYEILNNPELACTLAKTAFDEA.AELDTLNEDS
Retrocopy TIDNSQGAYQEAFHISKKEMQPTHPIGLGLALNFSVLYYEILNNPELACTLAKTAFDEALAELDTLNEDS

Parental  YKDSTLIMQLLRDNLTLWTSDSAGEECDAAEGAEN
          .KDSTLIMQLLRDNL.LWTSDSAGEE.D.AEGAEN
Retrocopy CKDSTLIMQLLRDNLALWTSDSAGEERDVAEGAEN

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	85.07 RPM
ERP005899_muscle	0.00 RPM	139.84 RPM
SRP017611_brain	0.05 RPM	218.30 RPM
SRP017611_kidney	0.00 RPM	154.94 RPM
SRP017611_liver	0.00 RPM	50.14 RPM
SRP030211_testis	0.13 RPM	389.70 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1180 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1180 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000236	4 retrocopies	retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Bos taurus	ENSBTAG00000002108	2 retrocopies	retro_btau_1180 , retro_btau_86,
Bos taurus	ENSBTAG00000005664	3 retrocopies	retro_btau_1485, retro_btau_372, retro_btau_954,
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Homo sapiens	ENSG00000134308	2 retrocopies	retro_hsap_3004, retro_hsap_8,
Gorilla gorilla	ENSGGOG00000001569	1 retrocopy	retro_ggor_2081,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mustela putorius furo	ENSMPUG00000013252	2 retrocopies	retro_mputfur_1132, retro_mputfur_730,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3,
Pteropus vampyrus	ENSPVAG00000005334	1 retrocopy	retro_pvam_983,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,