RetrogeneDB ID: retro_ecab_733

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:97063978..97064353(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000003658
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000015618
• Aliases: None
• Description: None

Sequence

>retro_ecab_733
ATGGCAATGCAAGCTGCCAAGAGGGCGAACATTCGACTTCCACTTGAAGTAAACCGGGTTTTGTATATAAGAAATTTGCC
GTGCAAAATCACAGCTGAAGAAATGTATGATATATTTGGAAAATATAGACCTACTCGTCAAATCAGAGTGGGGAACACAC
CTGAAACTAGGGGAACAGTTTATGTGGTCTATGAAGACGTCTTTGATGCCAAGAACACGTGTGATCACCTGTCAGGATTC
AATGTGTGTAACAGATACCTTGCGGTTTTGTACTATAGTGCTAACAGGGCATTTCAGAAGATGGGCACAAAGGAGAAGGA
AGAACAGTTGAAGCTTCTCGAAGAGAAATATGGCATCAACACAGATCCACCAAAG

Alignment

ORF - retro_ecab_733 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDA
          MAMQAAKRANIRLP.EVNR.LYIRNLP.KITAEEMYDIFGKY.P.RQIRVGNTPETRGT.YVVYED.FDA
Retrocopy MAMQAAKRANIRLPLEVNRVLYIRNLPCKITAEEMYDIFGKYRPTRQIRVGNTPETRGTVYVVYEDVFDA

Parental  KNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK
          KN.CDHLSGFNVCNRYL.VLYY.ANRAFQKM.TK.KEEQLKLL.EKYGINTDPPK
Retrocopy KNTCDHLSGFNVCNRYLAVLYYSANRAFQKMGTKEKEEQLKLLEEKYGINTDPPK

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	13.75 RPM
SRP021940_cerebellum	0.00 RPM	30.22 RPM
SRP021940_embryo	0.00 RPM	34.68 RPM
SRP021940_placental_villous	0.00 RPM	32.67 RPM
SRP021940_synovial_membrane	0.00 RPM	17.90 RPM
SRP021940_testis	0.00 RPM	24.30 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_733 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_733 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_733 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002786	1 retrocopy	retro_amel_1594,
Bos taurus	ENSBTAG00000003407	1 retrocopy	retro_btau_606,
Choloepus hoffmanni	ENSCHOG00000000689	3 retrocopies	retro_chof_1217, retro_chof_2457, retro_chof_351,
Callithrix jacchus	ENSCJAG00000007716	2 retrocopies	retro_cjac_2632, retro_cjac_487,
Dasypus novemcinctus	ENSDNOG00000007148	1 retrocopy	retro_dnov_1313,
Equus caballus	ENSECAG00000015618	1 retrocopy	retro_ecab_733 ,
Felis catus	ENSFCAG00000031365	1 retrocopy	retro_fcat_247,
Homo sapiens	ENSG00000115128	1 retrocopy	retro_hsap_1773,
Macaca mulatta	ENSMMUG00000001282	1 retrocopy	retro_mmul_1262,
Mustela putorius furo	ENSMPUG00000013957	1 retrocopy	retro_mputfur_882,
Nomascus leucogenys	ENSNLEG00000000815	1 retrocopy	retro_nleu_2806,
Otolemur garnettii	ENSOGAG00000004468	1 retrocopy	retro_ogar_2877,
Pongo abelii	ENSPPYG00000012603	2 retrocopies	retro_pabe_1098, retro_pabe_1461,
Pan troglodytes	ENSPTRG00000011709	1 retrocopy	retro_ptro_1187,
Sorex araneus	ENSSARG00000011902	1 retrocopy	retro_sara_638,