RetrogeneDB ID: retro_ecab_1033

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: Un0004:1253391..1254044(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000019846
• Aliases: None
• Description: None

Sequence

>retro_ecab_1033
CAAACAGAAGTTTTGGAGCTAAAGAATACAATAGAGAACTTCAACAGCACACTTGAACAAACAGAAGAGAGAATCAGCGA
GCTAGAAGGCAAATCAATTGAAATTATCCAGTCAGAGGAGAAAAAAGAAAAAGGAATGAAGAAAGCCTACGGGAATTATG
AAACATCATCAAAAGAAATAAGGTACACATAATTGGAGTCCCAGAAGAAGAAGAGAAAGGGATAGAAAGCTTATTTAAAG
AAATAATGGCTGAGAATTTCCCAAACCTAGGAAGAGATTTGGATATCCAAGTTCATGAAACTAATAGGTCGCCTCAAAGT
TTCAATCCAAAATGATCTTCTCCAAGACACATAATACTAAAATTGTCTACAACCAAAGACAAAGAGAAAATTAAAAGCAG
CAAGAGAAAAAAAATTTATTTCCTAAAAGGGAACCCCCATAAGGCTATCAGCAGATTTCTCAGCAGTGAACTTGCAGGTC
AGGAGAAAGTGGGATGATATATTCAGAATGTTAAAAGAAACTGCCCACCAAGAATACTTTAACCAGCAAAGTTGTTCTTC
AGAAATAAAGGAGAGATAAAGAATTTCCCAGATAAACAAAAAGTGAGAGAATTCGTCATCACTAAAGCTGCTTTACAAGA
AATGCTGAAGGGA

Alignment

ORF - retro_ecab_1033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.22 %
• Parental protein coverage: 98.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSAITEKKSSLNGFNSRFKQVEERINLLDDILEEITRAEQKEEKRIR-QNENSLRELWDNIKCANIHVIG
          .....E.K.....FNS...Q.EERI..L.....EI....Q.EEK.....NE.SLREL...IK....H.IG
Retrocopy QTEVLELKNTIENFNSTLEQTEERISELEGKSIEII---QSEEKKEK<RNEESLREL*NIIKRNKVHIIG

Parental  VPEERQRG-RKLFEEIIAEIFPNLRKETDTQVQEAQRVPNKTSPKRPTSRHIIIKMSKIKDKERILKAAR
          VPEE...G...LF.EI.AE.FPNL....D.QV.E..R.P....PK....RHII.K.S..KDKE.I.K...
Retrocopy VPEEEEKGIESLFKEIMAENFPNLGRDLDIQVHETNRSPQSFNPK*SSPRHIILKLSTTKDKEKI-KSSK

Parental  -ERQQVTYKGKPIRLSVDFSAKTLQVRREWHDIFKV-KEKNLQPRILYPARLSFTMEGEIKSFQDKQKLK
          .E......KG.PIRLS.DFSA..LQVRR.W.DIF......N..PRIL.PA.L.F...GEIK.F.DKQK..
Retrocopy >EKKFIS*KGTPIRLSADFSAVNLQVRRKWDDIFRM<VKRNCPPRIL*PAKLFFRNKGEIKNFPDKQKVR

Parental  EFITKKPILQEMLKG
          EF...K..LQEMLKG
Retrocopy EFVITKAALQEMLKG

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1033 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1033 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019846	8 retrocopies	retro_ecab_1033 , retro_ecab_391, retro_ecab_528, retro_ecab_531, retro_ecab_540, retro_ecab_574, retro_ecab_615, retro_ecab_918,