RetrogeneDB ID: retro_ecab_391

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:24750890..24751512(+)
• 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_391
AAAAATTCAACAGAGGGTTTCAACAGCAGACTAGATGAAGTGGAAGAAAGGATCAGTGAACTCGAAGACAGGGCAGTAGA
ATCCATTTAAACAGAGGAGCAAAAAGAAAAAAGAATGAAAAAGAGTGAATACAGCTTAAGGGACTTATGGGACAACATCA
AGTGGACTAATATTCACTTTGTAGAAGTCCCTGAAGGAGAGGAGAGCTTACGTGAAGAGATAATGGCTGAAAACTTCCCT
AACCTGGGGAAAGTAACAGACATCCAGATCCAGGAAGTCCAGACAGTTACAAATAAGATAAATCTGACAGACCCACACCA
AGACTCATTATACTTAATCTGTCAAAAGTTAAAGGAGAGATTATTAACAGTAACAAGAGGAAAACTACTTGTTGCATACA
AGGGAACTCCCACAAGACCATCAGCAGATTTTTCAGCAGAAATTTTGCAGGTCAGAAGGGAGTGGCATGATATATTCAAA
GTACCGAAACATAAAAACTGCCAGCCAAGAATACTCTACCTGGCCAAGTTTTACTTTAGAATTGAAGGAGAGAGAGAGTT
TTCCAGAGACGCAAAAGCTGAAGGAGTTCATCACTGGACAAGCCTTAGAAGAAATGTTAAAG

Alignment

ORF - retro_ecab_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.63 %
• Parental protein coverage: 95.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSSLNGFNSRFKQVEERINLLDDILEEITRAEQKEEKRIRQNENSLRELWDNIKCANIHVIGVPEERQRG
          K.S..GFNSR...VEERI..L.D...E....E..........E.SLR.LWDNIK..NIH...VPE.....
Retrocopy KNSTEGFNSRLDEVEERISELEDRAVESI*TEEXXXXXXXXSEYSLRDLWDNIKWTNIHFVEVPEGEE--

Parental  RKLFEEIIAEIFPNLRKETDTQVQEAQRVPNKTSPKRPTSRHIIIKMSKIKDKERILKAARERQQVTYKG
          ..L.EEI.AE.FPNL.K.TD.Q.QE.Q.V.NK.....P..........K.K..ER.L...R....V.YKG
Retrocopy -SLREEIMAENFPNLGKVTDIQIQEVQTVTNKINLTDPHQDSLYLICQKLK--ERLLTVTRGKLLVAYKG

Parental  KPIRLSVDFSAKTLQVRREWHDIFKV-KEKNLQPRILYPARLSFTMEGEIKSFQ-DKQKLKEFITKKPIL
          .P.R.S.DFSA..LQVRREWHDIFKV.K.KN.QPRILY.A...F..EGE...F....QKLKEFIT....L
Retrocopy TPTRPSADFSAEILQVRREWHDIFKVPKHKNCQPRILYLAKFYFRIEGE-REFS>ETQKLKEFITGQ-AL

Parental  QEMLK
          .EMLK
Retrocopy EEMLK

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_391 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_391 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_391 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,