RetrogeneDB ID: retro_btau_273

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:103069833..103070518(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC17
• Ensembl ID: ENSBTAG00000016818
• Aliases: None
• Description: nucleolar protein of 40 kDa [Source:RefSeq peptide;Acc:NP_001029824]

Sequence

>retro_btau_273
ATGAATTCAGGAAGACCCGAGACCATGGAGAACTTGCCTGCTCTGTACACTGTTTTCCAAGGAGAGGTTGCTAAGTCATA
GACTATGGAGCCTTTATCAAAATTCCAGGCTGTCAGAAGCAAGGTCTGATTTGAACTCACATGTCATCCTATTGCGTGGA
TAAGCCCTCTGAGATAGTAGATGTTGGAGACAAAGTGTGGATGAAGTTTACTGGCCGAGAGACAAAAAATGATAGGATAA
AATTATCCTTCTCCATGAAGGCTGTCAACTAAGGGACTGGGAAGGACCTTGATCCCAACAACATTATCACTGAGCAAGAA
GAGAGGCAGAGGCGGTCCTTCCAGGATTACACTGGGCAGAAGATCACCCTTGAGGCTGTCCTGAACACCACCTGCAAGAA
GTGTTGCTGTAAAAGCCACTTTGCAAAGGATTGTTTCATGCAACTAGGTGGGACCAAGTACTCTCCTATGAGGAAGAGAA
GGAAAAGGCAAAGTCAACAGAGTTTGAAAAGCCTGACACCATGAGAAATTCTTCTAGAAAAAGAAAGGAGAAATGTAAAC
ATAGAGACAGGAAGTCATCTGACTCTGACAGCTCAGTCTCTGAGAGTGATACAGGCAAGAAGACAAGGCACACATCAAAG
GACAGCAGGTCAGCAAAGAAGAAGACAAAGAAGAAGCACAAGGAG

Alignment

ORF - retro_btau_273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.82 %
• Parental protein coverage: 98.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNSGRPETMENLPALYTIFQGEVAM-VTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWV
          MNSGRPETMENLPALYT.FQGEVA..V.DYGAFIKIPGC.KQGL...THMSS..VDKPSEIVDVGDKVW.
Retrocopy MNSGRPETMENLPALYTVFQGEVAK<VIDYGAFIKIPGCQKQGLI*-THMSSYCVDKPSEIVDVGDKVWM

Parental  KLIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIEQEERRRRSFQDYTGQKITLEAVLNTTCKKCGCK
          K..GRE.KNDRIK.S.SMK.VN.GTGKDLDPNN.I.EQEER.RRSFQDYTGQKITLEAVLNTTCKKC.CK
Retrocopy KFTGRETKNDRIKLSFSMKAVN*GTGKDLDPNNIITEQEERQRRSFQDYTGQKITLEAVLNTTCKKCCCK

Parental  GHFAKDCFMQPGGTKYSLI-PDEEEEKEEAKSAEFEKPDTTRNSSRKRKKEKKKKKHRDRKSSDSDSSDS
          .HFAKDCFMQ.GGTKYS.....E.E.........FEKPDT.RNSSRKRK....K.KHRDRKSSDSDSS.S
Retrocopy SHFAKDCFMQLGGTKYSPM<EEEKEKAKSTE---FEKPDTMRNSSRKRK---EKCKHRDRKSSDSDSSVS

Parental  ESDTGKRARHTSKDSKAAKKKKKKKKHKK
          ESDTGK..RHTSKDS..A.KKK.KKKHK.
Retrocopy ESDTGKKTRHTSKDSRSA-KKKTKKKHKE

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	18.74 RPM
ERP005899_muscle	0.00 RPM	34.21 RPM
SRP017611_brain	0.14 RPM	49.88 RPM
SRP017611_kidney	0.00 RPM	17.13 RPM
SRP017611_liver	0.00 RPM	9.44 RPM
SRP030211_testis	0.00 RPM	58.50 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_273 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_273 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273 ,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218,
Dasypus novemcinctus	ENSDNOG00000000509	1 retrocopy	retro_dnov_2548,
Dipodomys ordii	ENSDORG00000004128	1 retrocopy	retro_dord_200,
Echinops telfairi	ENSETEG00000007421	1 retrocopy	retro_etel_1280,
Loxodonta africana	ENSLAFG00000015364	1 retrocopy	retro_lafr_534,
Myotis lucifugus	ENSMLUG00000000594	1 retrocopy	retro_mluc_2176,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mustela putorius furo	ENSMPUG00000015442	1 retrocopy	retro_mputfur_680,
Mus musculus	ENSMUSG00000028772	1 retrocopy	retro_mmus_2150,
Otolemur garnettii	ENSOGAG00000013749	1 retrocopy	retro_ogar_1225,
Sorex araneus	ENSSARG00000007944	1 retrocopy	retro_sara_691,
Ictidomys tridecemlineatus	ENSSTOG00000003825	1 retrocopy	retro_itri_405,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613,