RetrogeneDB ID: retro_ecab_558

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:54043161..54043887(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRAGD
• Ensembl ID: ENSECAG00000015826
• Aliases: None
• Description: Ras-related GTP binding D [Source:HGNC Symbol;Acc:19903]

Sequence

>retro_ecab_558
GACATGATCTTCAGGGGAACATGAGCACTGATATTTGTTATTGACTCTCGGGAGGATAACATGGAAGCCCTGGCCAGGCT
CCACCTCGTAGTCACCAGGGCCTACAAAGTAAACACCAGCATCAAATTTGAGGTGTTATTCACAAAGTAGATGGTCTGTC
AGATGACCACAAAATTGAAATCCATAGAGATACTCACCAGAGAGCAAATAATGACGTTGCAGATGCTGAATTAGAAAAAA
GCTCACCTCAGCTTTTATCTGACAACCATGTATGATTATTCAATATTTTAAGTTTTTAGCAAAGTGATTCAGAATTGATT
CCATATCTCTCAACCCTGGAGAATTTGCTGAACATCTTTATGTCAAATTCTGGAGTTGATAAGGCATTTCTGTTTCACGT
GGTCAGGAAAATTTATAATGCAACCGATAGTACCCAGCAAACCTATGAGCTCTGCTGTGATATGATAGATGTGTTATCGA
CATCTCTTGAATTTATGGTCTCAAAGAAGATGGAGCAGGAACTGCTAATGACAACAAATCAACAGCCATTATAAAGCTGA
ATATTACAACGGTTCTTTATTTAAAAGAAGTGACAATATTTCTGGCTCTTGTTGCTTTGTTGGAGATGAAAGCTTTGAAA
GAAAAGGTCTTATTGATTATAATTTTCATTGCTTCTGGAAGGCCATCCATGATGTTTTTGAGGTAAGAATGAAAATGGTG
AAATCT

Alignment

ORF - retro_ecab_558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.28 %
• Parental protein coverage: 70.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EMIFRGTGALIFVIDSQDDYMEALARLHLTVTRAYKVNTDINFEVF-IHKVDGLSDDHKIETQRDIHQRA
          .MIFRGT.ALIFVIDS..D.MEALARLHL.VTRAYKVNT.I.FEV..IHKVDGLSDDHKIE..RD.HQRA
Retrocopy DMIFRGT*ALIFVIDSREDNMEALARLHLVVTRAYKVNTSIKFEVL<IHKVDGLSDDHKIEIHRDTHQRA

Parental  NDDLADAGLEK-IHLSFYLTSIYDHSIFEAFSKVVQ-KLIPQLPTLENLLNIFISNSGIEKAFLFDVVSK
          N.D.ADA.LEK..HLSFYLT..YD.SIF..FSKV.Q..LIP.L.TLENLLNIF.SNSG..KAFLF.VV.K
Retrocopy NNDVADAELEK>AHLSFYLTTMYDYSIF*VFSKVIQ<ELIPYLSTLENLLNIFMSNSGVDKAFLFHVVRK

Parental  IYIATDSTPVDMQTYELCCDMIDV-VIDISCIYGLKEDGAGTPYDKESTAIIKLNNTTVLYLKEVTKFLA
          IY.ATDST....QTYELCCDMIDV.VIDIS.IYGLKEDGAGT..D..STAIIKLN.TTVLYLKEVT.FLA
Retrocopy IYNATDST---QQTYELCCDMIDV<VIDIS*IYGLKEDGAGTANDNKSTAIIKLNITTVLYLKEVTIFLA

Parental  LV-CFVREESFERKGLIDYNFHCFRKAIHEVFEVRMKVVKS
          LV.CFV..ESFERKGLIDYNFHCF.KAIH.VFEVRMK.VKS
Retrocopy LV<CFVGDESFERKGLIDYNFHCFWKAIHDVFEVRMKMVKS

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	0.35 RPM
SRP021940_cerebellum	0.00 RPM	10.13 RPM
SRP021940_embryo	0.00 RPM	4.14 RPM
SRP021940_placental_villous	0.00 RPM	6.11 RPM
SRP021940_synovial_membrane	0.00 RPM	0.99 RPM
SRP021940_testis	0.06 RPM	1.92 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_558 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018438	1 retrocopy	retro_btau_1643,
Choloepus hoffmanni	ENSCHOG00000001038	1 retrocopy	retro_chof_301,
Equus caballus	ENSECAG00000015826	1 retrocopy	retro_ecab_558 ,