RetrogeneDB ID: retro_ecab_574

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:19260581..19261244(-)
• 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_574
GAGATGAAAAACACAATAGATGAGATAAAGAAAAATCTGGACTCCCTAAACAACAAAACGGAGCATTTGGAAGACCAAAT
TAACAGTTTAGAAGACAATACTATAGAAATGCTTCAGAGGGAGGAGAAGAGAGAGCTAAGACTAAAAAGAAATGAAGAAG
CTCTCAGAGAAATATCTGACTCAATTAGAAAATGCAACATAAGGATTATAGGCATTCCAGAGGGGGAAGAGAAGGAGAAC
GAAGCAGAAAGCTTGTAATAGTGGAGATCTTCCCAAACCTGGGGAAAGAGATGGAAATCCATGTGAAAGAGGCTACCAGA
ACTCCCAACTATGTTAATGTAAAAAGACTACTACAAGGCATATTGTAATAAAGCTGGCAAAAGTCAATGACAAAGAAAAA
ATACTAAGGGCGGTAAGGCAGAAGAAAAGAACTTACAAAAGAACCCCTATCAGGCTTTCAGCAGATTTCTCAGCAGAAAC
CTTACAGGCTAGGAGAGAGTGGAATGATATATTTAAAATCCAGAAAGACAAAAAATTTCAGCCAAGAATACTCCATCCAG
TGAAAATCTCCTTCAGATATGATGGAGAAATAAAAACTTTCCAAGATAAACAAAAGCTCAGGGAGTTCATTGTCACAAGA
CTCCCCTACAAGAAATCCTCAAG

Alignment

ORF - retro_ecab_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.88 %
• Parental protein coverage: 99.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVKSAITEKKSSLNGFNSRFKQVEERINLLDDILEEITRAEQKEEKRIRQNENSLRELWDNIKCANIHVI
          E.K..I.E.K..L...N......E..IN.L.D...E....E.K.E.R...NE..LRE..D.I...NI..I
Retrocopy EMKNTIDEIKKNLDSLNNKTEHLEDQINSLEDNTIEMLQREEKRELRLKRNEEALREISDSIRKCNIRII

Parental  GVPEERQR-GRKLFEEIIAEIFPNLRKETDTQVQEAQRVPNKTSPKR-PTSRHIIIKMSKIKDKERILKA
          G.PE.....G.......I.EIFPNL.KE....V.EA.R.PN....KR..T.RHI.IK..K..DKE.IL.A
Retrocopy GIPEGEEK<GERSRKLVIVEIFPNLGKEMEIHVKEATRTPNYVNVKR<TTTRHIVIKLAKVNDKEKILRA

Parental  ARERQQVTYKGKPIRLSVDFSAKTLQVRREWHDIFKV-KEKNLQPRILYPARLSFTMEGEIKSFQDKQKL
          .R.....TYK..PIRLS.DFSA.TLQ.RREW.DIFK..K.K..QPRIL.P...SF...GEIK.FQDKQKL
Retrocopy VRQKKR-TYKRTPIRLSADFSAETLQARREWNDIFKIQKDKKFQPRILHPVKISFRYDGEIKTFQDKQKL

Parental  KEFIT-KKPILQEMLK
          .EFI...K..LQE.LK
Retrocopy REFIV<HKTPLQEILK

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_574 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_574 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,