RetrogeneDB ID: retro_ecab_273

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 12:18824505..18824995(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCUR1
• Ensembl ID: ENSECAG00000009150
• Aliases: None
• Description: mitochondrial calcium uniporter regulator 1 [Source:HGNC Symbol;Acc:21097]

Sequence

>retro_ecab_273
TTGGTCAAGATTATGGTAGGCAACATGAATATCGCCTACAAAAGATATGGTCACCATGGTCGCCATGCAGTAGCATATAA
TTCCACAGCAAATAATGTCTCAGATTGCTAATGTGAAAAAGGGTATGATTATTTTGGAGAAGAGCAAATTTTCATTTCTC
AGAGCATAAAATGAGAAAATAAAACTTGAACTACATCAGTTAAAATAACAAGTGATGGATGAACTGATCAAAGTCCAAAA
AGATGTCAAATTAGACGTCAGTCTAGAAAAGGGCAGAGTAAAAGAACTATATTCCTTGACCAAAAAGAAGCTGCTAGAAA
TGCGGACACAAATGGTGGCAGTGCATACCCAACAAGATCAGGCTCTCACCCAGACAGACAGGAAGACAGACGCTGAGGTT
GCTGGCCTCAAAACCATACTTGTGTCACAGAAGCTTAATAATATTAAATATTTAGCAGGGTCTATATTTACATGCCTAAC
ATCGGCTGTG

Alignment

ORF - retro_ecab_273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.56 %
• Parental protein coverage: 72.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVKIVEANMSIVYK-DMVTK--MQQEITLQQIMSQIANVKKDMIILEKSEFSALRAENEKIKLELHRLKQ
          LVKI...NM.I.YK.DMVT...MQ..I..QQIMSQIANVKK.MIILEKS.FS.LRA.NEKIKLELH.LK.
Retrocopy LVKIMVGNMNIAYK>DMVTMVAMQ*HIIPQQIMSQIANVKKGMIILEKSKFSFLRA*NEKIKLELHQLK*

Parental  QMMDEVVKVRTDTKLDFNLEKSRVKELYSLNERKLLEMRTEMVALHAQQDRAVTQTDRKIDTEVAGLKTM
          Q.MDE..KV..D.KLD..LEK.RVKELYSL...KLLEMRT.MVA.H.QQD.A.TQTDRK.D.EVAGLKT.
Retrocopy QVMDELIKVQKDVKLDVSLEKGRVKELYSLTKKKLLEMRTQMVAVHTQQDQALTQTDRKTDAEVAGLKTI

Parental  LESHKLDNIKYLAGSVFTCLTVAL
          L.S.KL.NIKYLAGS.FTCLT.A.
Retrocopy LVSQKLNNIKYLAGSIFTCLTSAV

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	2.13 RPM
SRP021940_cerebellum	0.00 RPM	5.61 RPM
SRP021940_embryo	0.00 RPM	6.04 RPM
SRP021940_placental_villous	0.00 RPM	12.75 RPM
SRP021940_synovial_membrane	0.00 RPM	8.89 RPM
SRP021940_testis	0.00 RPM	4.73 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_273 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_273 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_823

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000395	2 retrocopies	retro_amel_1628, retro_amel_473,
Canis familiaris	ENSCAFG00000009857	3 retrocopies	retro_cfam_1018, retro_cfam_1556, retro_cfam_823,
Callithrix jacchus	ENSCJAG00000016050	1 retrocopy	retro_cjac_2522,
Cavia porcellus	ENSCPOG00000014899	1 retrocopy	retro_cpor_934,
Equus caballus	ENSECAG00000009150	2 retrocopies	retro_ecab_273 , retro_ecab_469,
Felis catus	ENSFCAG00000005972	3 retrocopies	retro_fcat_1290, retro_fcat_1405, retro_fcat_1538,
Homo sapiens	ENSG00000050393	1 retrocopy	retro_hsap_1795,
Gorilla gorilla	ENSGGOG00000002632	1 retrocopy	retro_ggor_1320,
Loxodonta africana	ENSLAFG00000003287	2 retrocopies	retro_lafr_1252, retro_lafr_870,
Microcebus murinus	ENSMICG00000000183	2 retrocopies	retro_mmur_280, retro_mmur_580,
Myotis lucifugus	ENSMLUG00000010975	1 retrocopy	retro_mluc_1574,
Mustela putorius furo	ENSMPUG00000000698	1 retrocopy	retro_mputfur_640,
Nomascus leucogenys	ENSNLEG00000000914	1 retrocopy	retro_nleu_2768,
Otolemur garnettii	ENSOGAG00000013458	3 retrocopies	retro_ogar_1587, retro_ogar_1819, retro_ogar_3178,
Pan troglodytes	ENSPTRG00000017740	1 retrocopy	retro_ptro_1200,
Tarsius syrichta	ENSTSYG00000012562	1 retrocopy	retro_tsyr_810,
Tursiops truncatus	ENSTTRG00000012874	1 retrocopy	retro_ttru_1597,