RetrogeneDB ID: retro_btau_1637

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:15978605..15979256(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000018340
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZCRB1
• Ensembl ID: ENSBTAG00000019119
• Aliases: ZCRB1, MADP-1
• Description: Zinc finger CCHC-type and RNA-binding motif-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q56JZ7]

Sequence

>retro_btau_1637
ATGAGTGGTGGATTGGCCCCAAGTAAAAGCACAGTGTATGTATCCAATCTGCCCTTTTCCCTGACCAACAATGACTTATA
TCGGATATTTTCCAAGTATGGCAAAGTTGTAAAGGTTACTATAATGAAAGATAAAGATACCAGAAGGAGTAAAGGGGTTG
CATTTATTTTATTTTTGGATAAAGACTCTGCACAAAACTGTACCCGGGCAATAAACAACAAACAGTTATTTGGTAGAGTG
ATAAAAGCAAGCATTGCTATTGACAATGGAAGAGCAGCTGAGCTCATCCGAAGACGAAACTACTTTGATAAATCTAAGTG
TTATGAATGTGGGGAAAGTGGACACTTAAGTTATGCCTGTCCTAAAAATATGCTTGGAGAACAAGAACCTCCAAAGAAGA
AAGAGAAAAAGAAAAAAAAGAAAATTCCTGAGCCAGAAGAAGAAATTGAAGAAGTAGAAGAAAGTGAAGATGAAGGGGAA
GATCCTGCTCTTGACAGCCTCAGTCAGGCCATAGCTTTCCAGCAAGCCAAAATTGAAGAAGAACAAAAAAAATGGAAACC
CAGTTCAGGAGGTCCTTCAACATCAGATGATTCAAGATGCCCAAGGATAAAGAAAAGCACATACTTCAGTGATGAGGAGG
AACTTAGTGAT

Alignment

ORF - retro_btau_1637 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRRSKGVAFILFLDKDSAQNCTRA
          MSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRRSKGVAFILFLDKDSAQNCTRA
Retrocopy MSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRRSKGVAFILFLDKDSAQNCTRA

Parental  INNKQLFGRVIKASIAIDNGRAAEFIRRRNYFDKSKCYECGESGHLSYACPKNMLGEREPPKKKEKKKKK
          INNKQLFGRVIKASIAIDNGRAAE.IRRRNYFDKSKCYECGESGHLSYACPKNMLGE.EP..........
Retrocopy INNKQLFGRVIKASIAIDNGRAAELIRRRNYFDKSKCYECGESGHLSYACPKNMLGEQEPXXXXXXXXXX

Parental  KIPEPEEEIEEVEESEDEGEDPALDSLSQAIAFQQAKIEEEQKKWKPSSGGPSTSDDSRRPRIKKSTYFS
          ..PEP................PALDSLSQAIAFQQAKIEEE...WKPSSGGPSTSDDSR.PRIKKSTYFS
Retrocopy XXPEPXXXXXXXXXXXXXXXXPALDSLSQAIAFQQAKIEEEXXXWKPSSGGPSTSDDSRCPRIKKSTYFS

Parental  DEEELSD
          DEEELSD
Retrocopy DEEELSD

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	0.07 RPM	27.25 RPM
ERP005899_muscle	0.32 RPM	11.03 RPM
SRP017611_brain	0.18 RPM	13.52 RPM
SRP017611_kidney	0.06 RPM	21.28 RPM
SRP017611_liver	0.00 RPM	8.76 RPM
SRP030211_testis	0.45 RPM	15.44 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1637 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1637 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019119	2 retrocopies	retro_btau_1637 , retro_btau_830,
Choloepus hoffmanni	ENSCHOG00000004490	1 retrocopy	retro_chof_1549,
Callithrix jacchus	ENSCJAG00000017749	3 retrocopies	retro_cjac_2009, retro_cjac_2662, retro_cjac_4174,
Cavia porcellus	ENSCPOG00000014554	1 retrocopy	retro_cpor_757,
Dasypus novemcinctus	ENSDNOG00000010107	11 retrocopies	retro_dnov_1075, retro_dnov_1120, retro_dnov_1127, retro_dnov_1357, retro_dnov_1599, retro_dnov_1673, retro_dnov_1846, retro_dnov_2146, retro_dnov_2432, retro_dnov_2466, retro_dnov_888,
Equus caballus	ENSECAG00000012174	1 retrocopy	retro_ecab_184,
Erinaceus europaeus	ENSEEUG00000000397	1 retrocopy	retro_eeur_298,
Echinops telfairi	ENSETEG00000019302	1 retrocopy	retro_etel_2080,
Gorilla gorilla	ENSGGOG00000015647	1 retrocopy	retro_ggor_3029,
Loxodonta africana	ENSLAFG00000008847	2 retrocopies	retro_lafr_1183, retro_lafr_783,
Microcebus murinus	ENSMICG00000017422	3 retrocopies	retro_mmur_1236, retro_mmur_236, retro_mmur_466,
Myotis lucifugus	ENSMLUG00000001332	3 retrocopies	retro_mluc_2290, retro_mluc_319, retro_mluc_364,
Monodelphis domestica	ENSMODG00000008893	1 retrocopy	retro_mdom_114,
Mus musculus	ENSMUSG00000022635	1 retrocopy	retro_mmus_847,
Oryctolagus cuniculus	ENSOCUG00000013664	2 retrocopies	retro_ocun_742, retro_ocun_896,
Otolemur garnettii	ENSOGAG00000013178	2 retrocopies	retro_ogar_43, retro_ogar_812,
Ochotona princeps	ENSOPRG00000011095	2 retrocopies	retro_opri_729, retro_opri_927,
Procavia capensis	ENSPCAG00000011749	2 retrocopies	retro_pcap_458, retro_pcap_64,
Pan troglodytes	ENSPTRG00000004838	1 retrocopy	retro_ptro_3231,
Pteropus vampyrus	ENSPVAG00000006651	2 retrocopies	retro_pvam_1343, retro_pvam_697,