RetrogeneDB ID: retro_ecab_665

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 26:22034730..22035311(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000014612
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL1
• Ensembl ID: ENSECAG00000024511
• Aliases: None
• Description: mitochondrial ribosomal protein L1 [Source:HGNC Symbol;Acc:14275]

Sequence

>retro_ecab_665
AAGTCATATCACTATATGGAAAATGATCCTGAGGATGTCAATTTAAAACACTTGTACCTGTGGCAGATATATGAGGTGAA
GAAATCTATTCACATACTTAAAAATTTTCAAATTCTGGACTTTGTTAATCCAAAACAAGATGTTTATCTTGATTTGACAC
TGAATATTTCACTTGAGAAAAAGATAAAAGTGGAGCCATTTGCCACTGTTCTTAGTTTTCCATATCCATTCACATCAGAA
ATCAATAAAGTTGCTGCATCTAAAGGAAATGCATCAGAGATTAAAACAGCAGAAGAAAACAGAGGTGCCTTTGCAGAAAG
AACTAATCTGATTCAGAGGATTTTGCATGATGAAATTCATGTAGACGTTTATGTATCTGTTTAGAAATAACGTCAGAGAT
TAATCCATTAGAAAAGAAACTGATAAAAGATTTTTCAAAATTTATTCAAAATTCCTTTGACCTTGACATTCACCAAATGC
TAGAATTGTTTAAAACTGGGCGTGAAATTAAGGTATATGAAGAAAGGGAGAACTTTCTAGAAACCAAAATAGCAACATTG
GATCAAGTGACCAGACAGCTG

Alignment

ORF - retro_ecab_665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.35 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSYPFMEGEPEDDVYLKHLYPRQIYDVEKAIHLLKKFQILDFTNPKQGVYLDLTLDMALGKKKKVEPFAS
          KSY..ME..PED.V.LKHLY..QIY.V.K.IH.LK.FQILDF.NPKQ.VYLDLTL...L.KK.KVEPFA.
Retrocopy KSYHYMENDPED-VNLKHLYLWQIYEVKKSIHILKNFQILDFVNPKQDVYLDLTLNISLEKKIKVEPFAT

Parental  VLSFPYPFISEINKVAVFTRNASEIKVAEENGAAIAGGTDVIQKILDDEIQLDFYVAV-PEIMPELNPLK
          VLSFPYPF.SEINKVA....NASEIK.AEEN..A.A..T..IQ.IL.DEI..D.YV.V..EI..E.NPL.
Retrocopy VLSFPYPFTSEINKVAASKGNASEIKTAEENRGAFAERTNLIQRILHDEIHVDVYVSV<LEITSEINPLE

Parental  KKLKKRFPKLAQNSIGRDIPKMLELFKTGHEIKVDEERENFLKTKIATLDMSSDQI
          KKL.K.F.K..QNS...DI..MLELFKTG.EIKV.EERENFL.TKIATLD....Q.
Retrocopy KKLIKDFSKFIQNSFDLDIHQMLELFKTGREIKVYEERENFLETKIATLDQVTRQL

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	1.18 RPM
SRP021940_cerebellum	0.00 RPM	0.42 RPM
SRP021940_embryo	0.00 RPM	3.76 RPM
SRP021940_placental_villous	0.00 RPM	1.88 RPM
SRP021940_synovial_membrane	0.00 RPM	1.56 RPM
SRP021940_testis	0.00 RPM	1.15 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_665 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_665 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_665 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000024511	1 retrocopy	retro_ecab_665 ,
Myotis lucifugus	ENSMLUG00000011011	2 retrocopies	retro_mluc_2466, retro_mluc_534,
Pteropus vampyrus	ENSPVAG00000002696	2 retrocopies	retro_pvam_67, retro_pvam_913,
Tursiops truncatus	ENSTTRG00000011899	1 retrocopy	retro_ttru_1405,