RetrogeneDB ID: retro_btau_1004

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:16937590..16937972(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD1
• Ensembl ID: ENSBTAG00000009689
• Aliases: None
• Description: RWD domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001029898]

Sequence

>retro_btau_1004
AATAAAATTAAGTGAAATGGTAGATCAAATAGAAACCTGAAGACGAGAAGAAGAGCAGAAGCTGAAAAACAATTATTTTA
TGGTACTCCTATTACTATTCAAAATTTCTTAAGTTGAAAGGCCAAGTTTGATACAGAACTCTTGGAAATGTTTTTAAATG
AATGAAAGTAAAGGAACAAGCAGGAAAAAGTAAATTAAGTGGGAAACAGCTGTTTGAAACAGATCATAATCCTGACACAG
CTAATATCCAGTTCTTGGAGGATGCTGGATACAGCGTGGAGGTAGATGAGTCACTTGTCCAGAAATTAAATGACTTGGAT
CCAGAGGATAAGGAGGATGATCCAGACTACAATCCTGCTGACCAGAGAGTGATTTGACCAAC

Alignment

ORF - retro_btau_1004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.85 %
• Parental protein coverage: 52.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DQIKTRREEEKKQKEKEAEEAEKQLFHGTPVTIENFLNWKAKFDAELLEIKK-KRMKEEEQAGKNKLSGR
          ..IK.........K.....EAEKQLF.GTP.TI.NFL..KAKFD.ELLE....K.MK..EQAGK.KLSG.
Retrocopy NKIK*NGRSNRNLKTRRRAEAEKQLFYGTPITIQNFLS*KAKFDTELLEMFL<K*MKVKEQAGKSKLSGK

Parental  QLFETDHNLDTSDIQFLEDAGNNVEVDESLFQEMDDLELEDDDDDPDYNPADR-ESDLTD
          QLFETDHN.DT..IQFLEDAG..VEVDESL.Q...DL..ED..DDPDYNPAD..ESDLT.
Retrocopy QLFETDHNPDTANIQFLEDAGYSVEVDESLVQKLNDLDPEDKEDDPDYNPADQ<ESDLTN

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	39.00 RPM
ERP005899_muscle	0.00 RPM	34.31 RPM
SRP017611_brain	0.00 RPM	17.95 RPM
SRP017611_kidney	0.00 RPM	34.97 RPM
SRP017611_liver	0.00 RPM	21.22 RPM
SRP030211_testis	0.00 RPM	125.95 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1004 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1004 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005692	1 retrocopy	retro_amel_991,
Bos taurus	ENSBTAG00000009689	1 retrocopy	retro_btau_1004 ,
Callithrix jacchus	ENSCJAG00000004474	1 retrocopy	retro_cjac_1622,
Equus caballus	ENSECAG00000006587	2 retrocopies	retro_ecab_216, retro_ecab_277,
Echinops telfairi	ENSETEG00000019085	3 retrocopies	retro_etel_140, retro_etel_1992, retro_etel_423,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686,
Oryctolagus cuniculus	ENSOCUG00000013592	1 retrocopy	retro_ocun_691,
Procavia capensis	ENSPCAG00000005016	1 retrocopy	retro_pcap_114,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Ictidomys tridecemlineatus	ENSSTOG00000022124	1 retrocopy	retro_itri_596,
Tupaia belangeri	ENSTBEG00000002543	2 retrocopies	retro_tbel_2986, retro_tbel_4366,