RetrogeneDB ID: retro_ecab_292

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:8758221..8758640(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSECAG00000001043
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:HGNC Symbol;Acc:13870]

Sequence

>retro_ecab_292
GTACCCCATGTGTTCCTGCTGCAGCTGGGGACAACTTTCTTCAAAGCGTTGGGTGGTGAACTTAACCCAGGAGAAGACGA
AGAGGAAGAAGGTGAATTTGAAGGACCAAAACTCCTACTGACAGACATACTGGGTGGTTGAAGTGGAGTCCCGCCAGACT
GGGTCATGATGCCTGCACGGGTAACCAGTAGGGACCAAATTTGGAGCCTCCTCAGTATGCATATATTCCTGCACATATTA
CAAAGCCTCCAGAACAGAAGAAGTTGTTTTTCATTCAACTTCAAGAGAAAGCCTTGTCTGAGGCCCCTAAAAATTACAAG
TCGACAGCTGCACCACTGTTTGAACTGAGTGCCCAGGCACCAGGCTGTGGACCCGTCAGTTTTCATCTCCCTTGGCTTCT
GAGCAGGTTCAGTTTTCTA

Alignment

ORF - retro_ecab_292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.99 %
• Parental protein coverage: 59.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPHVLLLQLG-TTFFKLPG----GELNPGEDEVEGLKRLMTEILGRQDGVLQDWVI-DDCIGNWWRPNFE
          .PHV.LLQLG.T.F..L.G....GE....E.E.EG.K.L.T.ILG...GV..DWV..D.C.GN...PN.E
Retrocopy VPHVFLLQLGTTFFKALGGELNPGEDEEEEGEFEGPKLLLTDILGG*SGVPPDWVM<DACTGNQ*GPNLE

Parental  PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNF
          PPQY.YIPAHITKP.E.KKLF..QLQEKAL...PKNYK..AAPLFEL...APG.GP....LP.LLSRF.F
Retrocopy PPQYAYIPAHITKPPEQKKLFFIQLQEKALSEAPKNYKSTAAPLFELSAQAPGCGPVSFHLPWLLSRFSF

Parental  I
          .
Retrocopy L

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
SRP021940_articular_cartilage	0.00 RPM	38.90 RPM
SRP021940_cerebellum	0.21 RPM	19.89 RPM
SRP021940_embryo	0.49 RPM	55.44 RPM
SRP021940_placental_villous	0.05 RPM	29.16 RPM
SRP021940_synovial_membrane	0.44 RPM	27.75 RPM
SRP021940_testis	1.41 RPM	161.33 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_292 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_292 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_292 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016628	1 retrocopy	retro_amel_540,
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Equus caballus	ENSECAG00000001043	1 retrocopy	retro_ecab_292 ,
Erinaceus europaeus	ENSEEUG00000003402	1 retrocopy	retro_eeur_35,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Myotis lucifugus	ENSMLUG00000004968	2 retrocopies	retro_mluc_1576, retro_mluc_999,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tupaia belangeri	ENSTBEG00000007664	1 retrocopy	retro_tbel_4003,
Vicugna pacos	ENSVPAG00000003701	2 retrocopies	retro_vpac_340, retro_vpac_605,