RetrogeneDB ID: retro_ecab_383

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:51281085..51281958(-)
• Located in intron of: ENSECAG00000011942

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A30
• Ensembl ID: ENSECAG00000017334
• Aliases: None
• Description: solute carrier family 25, member 30 [Source:HGNC Symbol;Acc:27371]

Sequence

>retro_ecab_383
ATGGCGGCCCTCAACCGGAAGCCCTTTGTGTACGGAGGGCTGGCCTCCATCCCGGCAGAATGCGGTACATTCCCAATTGA
TTTAACCAAGATGTGGCTCCAGATTCAATGGCAGACGAACGACGCCAACTTGAAAGAAATCCGGTACAGAGGCGTGTTGC
ATGCTTTCGTGACGATAGGCCGAGAGGAAGGGCTGAAAGCGCTGTAGGTCGGGATTGCCCCCGCGATGCTACGCCAGGCT
TCCTATGGCACCGTCAAGATAGGCACTTAGCAGAGCTTGAAGCGATTATTTGTCGAACGCCCAGAAGGTGAGACTCTACT
GATAAATGTGGTCTGTGGAATTCTCTCTGGAGTCCTATCCTCAGCCATTGCTAATCCAACTGATGTTTTGAAAATACGGA
TGCAAGCACAAAGCAGCAGCATTCAGGGAGGAATGATAGGCAGCTTCATTAACAATTACCAGCAAGAGGGACCGAGAGGA
CTGTGGAAGGGCGTGTCCCTTACCGCTCAGAGGGCTCCTATTGTTGTTGGCTTGGAGCTGCGGGTCTGCGACCTCGCCAA
GAAGCATCTGATCCTCTGGGGCCTGATGGGAGACCCTGTGTCTACCCACTTCCTCTCAAGCTTCACCTGAGGTCTGGCCG
GGGCCCTGGCCTCAAACCCTGTCGAAGTTGTGAGAACACCTGTGATGAATCAGAGAGTCCTTCGAGATGGCACATGCTGT
GGCTACACGGGTACCCTGGATTGCTTGTTACAGACTTGGAAGAATGAAGGGCTTTTTGCTCTATATAAAGGGTTTTGGCC
AAATTGGTTGAGACTTGGACCTTGGAACATCATTTTCTTTGTGACATGTGAGCGGCTGAAGAAACTGGATTTG

Alignment

ORF - retro_ecab_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSALNWKPFVYGGLASITAECGTFPIDLTKTRLQIQGQTNDANFKEIRYRGMLHALVRIGREEGLKALYS
          M.ALN.KPFVYGGLASI.AECGTFPIDLTK..LQIQ.QTNDAN.KEIRYRG.LHA.V.IGREEGLKAL..
Retrocopy MAALNRKPFVYGGLASIPAECGTFPIDLTKMWLQIQWQTNDANLKEIRYRGVLHAFVTIGREEGLKAL*V

Parental  GIAPAMLRQASYGTIKIGTYQSLKRLFVERPEDETLLINVVCGILSGVISSTIANPTDVLKIRMQAQSST
          GIAPAMLRQASYGT.KIGT.QSLKRLFVERPE.ETLLINVVCGILSGV.SS.IANPTDVLKIRMQAQSS.
Retrocopy GIAPAMLRQASYGTVKIGT*QSLKRLFVERPEGETLLINVVCGILSGVLSSAIANPTDVLKIRMQAQSSS

Parental  IQGGMIGNFINIYQQEGTRGLWKGVSLTAQRAAIVVGVELPVYDLTKKHLILSGLMGDTVYTHFLSSFTC
          IQGGMIG.FIN.YQQEG.RGLWKGVSLTAQRA.IVVG.EL.V.DL.KKHLIL.GLMGD.V.THFLSSFT.
Retrocopy IQGGMIGSFINNYQQEGPRGLWKGVSLTAQRAPIVVGLELRVCDLAKKHLILWGLMGDPVSTHFLSSFT*

Parental  GLAGALASNPVDVVRTRMMNQRVLRDGSCPGYTGTLDCLLQTWKNEGFFALYKGFWPNWLRLGPWNIIFF
          GLAGALASNPV.VVRT..MNQRVLRDG.C.GYTGTLDCLLQTWKNEG.FALYKGFWPNWLRLGPWNIIFF
Retrocopy GLAGALASNPVEVVRTPVMNQRVLRDGTCCGYTGTLDCLLQTWKNEGLFALYKGFWPNWLRLGPWNIIFF

Parental  VTYEQLKKLDL
          VT.E.LKKLDL
Retrocopy VTCERLKKLDL

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	7.14 RPM
SRP021940_cerebellum	0.05 RPM	12.20 RPM
SRP021940_embryo	0.00 RPM	12.20 RPM
SRP021940_placental_villous	0.05 RPM	9.29 RPM
SRP021940_synovial_membrane	0.00 RPM	7.06 RPM
SRP021940_testis	0.13 RPM	92.33 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_383 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_383 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017334	1 retrocopy	retro_ecab_383 ,