RetrogeneDB ID: retro_btau_461

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:16278021..16279003(+)
• Located in intron of: ENSBTAG00000007079

Retrocopy information

• Ensembl ID: ENSBTAG00000046444
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.69182
• Ensembl ID: ENSBTAG00000014804
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:RefSeq peptide;Acc:NP_001077194]

Sequence

>retro_btau_461
ACAATAGAACGCTCCTCCGCCACTGCGGCCGCGACTTGGTCTCAGCGCCAGGACCCTCCGGCGGACCACTCCGCAGCTAT
GGAAGACATGAACGAGTACAGCAACATAGAAGAATTCGCAGAGGGATCCAAGATCAACGCGAGCAAGAACCAGCAGGATG
ACGGTAAAATGTTTATTGGAGGTTTGAGCTGGGATACAAGCAAGAAAGATCTAACTGAATATTTGTCTCGATTTGGGGAA
GTTGTGGACTGCACGATGAAAACAGATCCTGTTACTGGAAGATCAGGAGGATTTGGATTTGTGCTTTTCAAGCATGCTGC
TAGTGTTGATAAGGTTTTGGAACTGAAAGAACACAAACTGGATGGCAAATTGATAGACCCTAAAAGGGCCAAAGTTTTAA
AGGGGAAGGAACCCCCAAAAAAGGTTTTCGTGGGTGGATTGAGCCCAGATACTTCGGAGGAACAAATTAAAAGAATATTT
TGGAGCCTTTGGAGAGATTGAAAATATTGAACTTCCTGTGGATACAAAAACAAATGAAAGAAGAGGATTTTGCTTTATTA
CATACATAGACGAGGAGCCAGTAAAGAAATTGTTAGAAAGCAGATACCATCAAACTGGTTCTGGGAAGTGTGAAATCAAA
GTTGCACAACCCAAAGAGGTATATAGCCAGCAACAGCAGCAACAAAAGGGAGGAAGAGGTGCTGCAGCTGGTGGGCGAGG
TGGTACTAGGGCTCGAGGCCGAGGTCAGGGCCAAAACTGGAACCAAGGATTTAATAACTATCATGATCAAGGATATGGAA
ATTACAATGGTGCCTATGGTGGTGATCAAAACTGTAGTGGCTATGGCGGCTATGATTATACTGGGTATAACTATGGGAAC
TATGGATATGGACGGGGATATGCAGACTACAGTGGCCAACAGAGCACTTACGGCAAGGCATCCCGAGGGGGTGGCAATCA
CCAAAACAATTACCAGCCGTAT

Alignment

ORF - retro_btau_461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 77.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SIQRSAAAAAATRSARQHLPADHSAAMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGGLSWDTSKKD
          .I.RS.A.AAAT.S.RQ..PADHSAAMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGGLSWDTSKKD
Retrocopy TIERSSATAAATWSQRQDPPADHSAAMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGGLSWDTSKKD

Parental  LTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKALKGKEPPK
          LTEYLSRFGEVVDCT.KTDPVTGRS.GFGFVLFK.AASVDKVLELKEHKLDGKLIDPKRAK.LKGKEPPK
Retrocopy LTEYLSRFGEVVDCTMKTDPVTGRSGGFGFVLFKHAASVDKVLELKEHKLDGKLIDPKRAKVLKGKEPPK

Parental  KVFVGGLSPDTSEEQIK-EYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRYHQIGSGK
          KVFVGGLSPDTSEEQIK.EYFGAFGEIENIELP.DTKTNERRGFCFITY.DEEPVKKLLESRYHQ.GSGK
Retrocopy KVFVGGLSPDTSEEQIK>EYFGAFGEIENIELPVDTKTNERRGFCFITYIDEEPVKKLLESRYHQTGSGK

Parental  CEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYNSAYGGDQNYS
          CEIKVAQPKEVY.QQQQQQKGGRGAAAGGRGGTR.RGRGQGQNWNQGFNNY.DQGYGNYN.AYGGDQN.S
Retrocopy CEIKVAQPKEVYSQQQQQQKGGRGAAAGGRGGTRARGRGQGQNWNQGFNNYHDQGYGNYNGAYGGDQNCS

Parental  GYGGYDYTGYNYGNYGYGQGYADYSGQQSTYGKASRGGGNHQNNYQPY
          GYGGYDYTGYNYGNYGYG.GYADYSGQQSTYGKASRGGGNHQNNYQPY
Retrocopy GYGGYDYTGYNYGNYGYGRGYADYSGQQSTYGKASRGGGNHQNNYQPY

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	155.44 RPM
ERP005899_muscle	0.21 RPM	50.73 RPM
SRP017611_brain	0.05 RPM	171.57 RPM
SRP017611_kidney	0.12 RPM	147.82 RPM
SRP017611_liver	0.00 RPM	61.09 RPM
SRP030211_testis	0.21 RPM	135.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_461 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_461 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001553	20 retrocopies	retro_btau_1019, retro_btau_1065, retro_btau_1268, retro_btau_1378, retro_btau_1379, retro_btau_1437, retro_btau_1455, retro_btau_1657, retro_btau_1673, retro_btau_283, retro_btau_337, retro_btau_403, retro_btau_462, retro_btau_516, retro_btau_519, retro_btau_589, retro_btau_602, retro_btau_677, retro_btau_715, retro_btau_822,
Bos taurus	ENSBTAG00000005726	4 retrocopies	retro_btau_1330, retro_btau_1535, retro_btau_193, retro_btau_228,
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461 ,
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Cavia porcellus	ENSCPOG00000015619	5 retrocopies	retro_cpor_1110, retro_cpor_1318, retro_cpor_264, retro_cpor_274, retro_cpor_567,
Equus caballus	ENSECAG00000022692	1 retrocopy	retro_ecab_1082,
Microcebus murinus	ENSMICG00000001445	4 retrocopies	retro_mmur_1016, retro_mmur_1570, retro_mmur_1572, retro_mmur_557,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ochotona princeps	ENSOPRG00000007178	3 retrocopies	retro_opri_1075, retro_opri_623, retro_opri_703,
Procavia capensis	ENSPCAG00000011543	1 retrocopy	retro_pcap_366,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,
Sorex araneus	ENSSARG00000009961	1 retrocopy	retro_sara_421,