RetrogeneDB ID: retro_ecab_664

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 26:13974203..13974856(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMX2
• Ensembl ID: ENSECAG00000008257
• Aliases: None
• Description: RNA binding motif protein, X-linked 2 [Source:HGNC Symbol;Acc:24282]

Sequence

>retro_ecab_664
TTAGCCACGGTGAAGCTGGTTAGCCAGCTGAGTGAGTGGGAGGCCGACACGGCCATGGCTGCGAAGGCGAACTGGCGCTC
AGTGTAGAAGGACAGCGCCTGGGTCTTCCTGGGAGCGTTTCCTTATGAGCTGACGGAAGGAGACGTCCTCTGCGTGTTCT
CCCTGTACGGGGAGATTGTTAACGTTAATCTCGTGCGGGCCGGGAAGACAGGGAAGTCTAAAGGATTCTGCTTTCTCTGT
TATGAAGACCAGAGGAGTACAGTTTTGGCCGTTGACAGTCTTAATGGCGTCAAGATCAAGGGAAGAGCTATCCGAGTGGA
CCACGTATCCCGCTCCCGCCCCCCTCGGGCCTCACAGGATGTGGATGACGCCACCAGAGAGCTCTGGGCGAAGGGCTGCG
GGGCTGAGACCCCTCATCCAGTTCATCTGAGGGCTCTGAAGACGAAGCCCTCTCAGCACAGCACAAACAAGAAAAACAGA
CAAGAAAAAAGACCGAAGAGAAGACTGTTGTATTAGTTAAAGAGGAAGAGGGACAGTCAGAGCAGCCCTCGTCCCTGCCA
GCCGGAGGCCAGACTGAAATGGAGAGGGACGCCCCAGGCTCCGATAAACAAACCCAGGTAAAGTTAGGGTCTAGAGAGGG
CCAGAAACCTGAC

Alignment

ORF - retro_ecab_664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.66 %
• Parental protein coverage: 87.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTKVKLINELNEREVQLGVADKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYGEIVNINLVRDKKT
          L..VKL...L.E.E.....A.K..W.S..KDSAW.FLG..PYELTEGD..CVFS.YGEIVN.NLVR..KT
Retrocopy LATVKLVSQLSEWEADTAMAAKANWRSV*KDSAWVFLGAFPYELTEGDVLCVFSLYGEIVNVNLVRAGKT

Parental  GKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVSNYRAPKDSEEMDDVSKGLQEKGCGARTPSP
          GKSKGFCFLCYEDQRST.LAVD..NG.KIKGR.IRVDHVS..R.P..S...DD....L..KGCGA.TP.P
Retrocopy GKSKGFCFLCYEDQRSTVLAVDSLNGVKIKGRAIRVDHVSRSRPPRASQDVDDATRELWAKGCGAETPHP

Parental  -SSSEGSEDDKPTKKHKKDKKEKKKRKKDKEKTDREVQEEQPAS---SSSPR-SKTIKEKDDPGSKKHS-
          .SSSEGSED......HK....EK..RKK..EKT...V.EE...S...SS.P....T..E.D.PGS.K...
Retrocopy <SSSEGSEDEALSAQHK---QEKQTRKKTEEKTVVLVKEEEGQSEQPSSLPAGGQTEMERDAPGSDKQTQ

Parental  -SKNSERGQKSE
          ....S..GQK..
Retrocopy VKLGSREGQKPD

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	2.95 RPM
SRP021940_cerebellum	0.00 RPM	4.36 RPM
SRP021940_embryo	0.00 RPM	4.17 RPM
SRP021940_placental_villous	0.00 RPM	1.54 RPM
SRP021940_synovial_membrane	0.00 RPM	4.09 RPM
SRP021940_testis	9.72 RPM	1.34 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_664 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_664 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_664 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_106

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002436	2 retrocopies	retro_cjac_3040, retro_cjac_4128,
Equus caballus	ENSECAG00000008257	1 retrocopy	retro_ecab_664 ,
Equus caballus	ENSECAG00000009325	1 retrocopy	retro_ecab_19,
Echinops telfairi	ENSETEG00000001763	1 retrocopy	retro_etel_1004,
Myotis lucifugus	ENSMLUG00000017095	1 retrocopy	retro_mluc_310,
Sarcophilus harrisii	ENSSHAG00000016412	1 retrocopy	retro_shar_2,