RetrogeneDB ID: retro_ecab_720

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:61904142..61904475(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf73
• Ensembl ID: ENSECAG00000015605
• Aliases: None
• Description: chromosome 11 open reading frame 73 [Source:HGNC Symbol;Acc:26938]

Sequence

>retro_ecab_720
AAAATTGCATGCCTTAAATCTGGAGAAGGAAGCCGACACCCCTCTGGAGCCATGAATATTGTCCAGACTCCATCTGTTGC
TCTGATTGGAATTTCAGCAGATTTACAGACTCAGACTGCTGTGGGGGATGCTGCTGACTCCTTAGCTGATTCATTCACTC
AGCCATCCATGAAACGTGGGGCAATGTCTACTGCTCTGCTTCATCATTTGCTCTTTCTGAGGCCTAGATGACACCAAATC
CATCTGAATTTTTCATTCCAGCAAGTGAGGCTCAGCCAACGTTATGAAAATTTTCAAAGATGACTAACATTGAGTCCTCT
CCTCTGAAAAACA

Alignment

ORF - retro_ecab_720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.97 %
• Parental protein coverage: 58.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KISGLKSGEGSQHPFGAMNIVRTPSVAQIGISVELLDSLAQQTPVGNAAVSSVDSFTQFTQK-MLDNFYN
          KI..LKSGEGS.HP.GAMNIV.TPSVA.IGIS..L....A....VG.AA.S..DSFTQ...K....N.Y.
Retrocopy KIACLKSGEGSRHPSGAMNIVQTPSVALIGISADLQTQTA----VGDAADSLADSFTQPSMK<TWGNVYC

Parental  FASSFAVSQAQMTPSPSEMFIPANV-VLKWYENFQRRLAQNPLFWKT
          .ASSFA.S.A.MTP.PSE.FIPA.......YENFQR.L...PL..KT
Retrocopy SASSFALSEA*MTPNPSEFFIPASE>LSQRYENFQR*LTLSPLL*KT

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	7.73 RPM
SRP021940_cerebellum	0.00 RPM	13.40 RPM
SRP021940_embryo	0.00 RPM	18.62 RPM
SRP021940_placental_villous	0.00 RPM	14.96 RPM
SRP021940_synovial_membrane	0.00 RPM	11.12 RPM
SRP021940_testis	0.06 RPM	8.76 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_720 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_720 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015605	1 retrocopy	retro_ecab_720 ,
Homo sapiens	ENSG00000149196	1 retrocopy	retro_hsap_4658,
Gorilla gorilla	ENSGGOG00000023168	1 retrocopy	retro_ggor_2891,
Myotis lucifugus	ENSMLUG00000016260	1 retrocopy	retro_mluc_784,
Mus musculus	ENSMUSG00000062797	1 retrocopy	retro_mmus_3722,
Nomascus leucogenys	ENSNLEG00000016224	1 retrocopy	retro_nleu_1095,
Oryctolagus cuniculus	ENSOCUG00000013108	2 retrocopies	retro_ocun_1147, retro_ocun_280,
Pongo abelii	ENSPPYG00000003746	1 retrocopy	retro_pabe_3618,
Pan troglodytes	ENSPTRG00000004144	1 retrocopy	retro_ptro_3094,
Tupaia belangeri	ENSTBEG00000009192	2 retrocopies	retro_tbel_1594, retro_tbel_3248,
Tursiops truncatus	ENSTTRG00000012267	1 retrocopy	retro_ttru_562,