RetrogeneDB ID: retro_ecab_531

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:119501113..119501773(-)
• 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_531
AAATCATAAATCTGAAGAACTAAAAAATTCAATAGAGGGGTCAAGAGCAGACTAGATGAAGCAGAAAAAAGGATCAGCAA
ATGCAAAGATAGGGCAGTGGAATTCATCTACTCAAAGCAGCAAAGACAGTGAAAAGGAGTGAAGACAGCTGACAAGATTA
AACGGACACTATCAAGTGGACTTATAGTCACATATGGGGTCCCACAAGGAGAAGAGAGAGAGAAAAGAGCAAAAAACTTA
TCTGAAGGAATAACGGCTGAAAATTTCCCTACCCTGGAGGAGGAAACAGACATCCAGATCCAGGAAGCCCAGAGAGTTCC
AAATAAGATGAACCCAAAGAGATCACACCAAGACACATTATAATCAAATTATCAAAAGTTAAAGACAAGGAGAGAATCTT
AAAAGCAGCAAGAGAAAAACAACTTATTATGTACAAGGGAACCCCCATAAAACTGTCAGCAGATTTTTCAGCAGAAACTT
TGCAGGACAAAAGGGAGTGGCACAATATATTCAAAGTGCTGAAAGAAAAAAAAACTACCAACCAAGAATACTCCAGCAAA
GTTGTCCTTTAGAAATGAAGGAGAGATAAAGAGTTTTCCAGACAAACAAAAGCTGAAGGAGTTCATAACCACAAGACTGA
CTCTATAAGAAGTGTTAAAG

Alignment

ORF - retro_ecab_531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.21 %
• Parental protein coverage: 98.21 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSAITEKKSSLNGFNSRFKQVEERINLLDD-ILEEITRAEQKEEKRIRQNENSLRELWDNIKCANIHVIG
          KS.I...K....G..SR....E.RI....D...E.I....Q...K.........R.L........I...G
Retrocopy KS*I*RTKKFNRGVKSRLDEAEKRISKCKDRAVEFIYSKQQRQ*KGVKTADKIKRTLSSGL----IVTYG

Parental  VP---EERQRGRKLFEEIIAEIFPNLRKETDTQVQEAQRVPNKTSPKRP-TSRHIIIKMSKIKDKERILK
          VP...E...R...L.E.I.AE.FP.L..ETD.Q.QEAQRVPNK..PKR..T.RHIIIK.SK.KDKERILK
Retrocopy VPQGEEREKRAKNLSEGITAENFPTLEEETDIQIQEAQRVPNKMNPKRS<TPRHIIIKLSKVKDKERILK

Parental  AARERQQVTYKGKPIRLSVDFSAKTLQVRREWHDIFKVKEKNLQPRILY-PARLSFTMEGEIKSFQDKQK
          AARE.Q...YKG.PI.LS.DFSA.TLQ..REWH.IFKV..........Y.PA.LSF..EGEIKSF.DKQK
Retrocopy AAREKQLIMYKGTPIKLSADFSAETLQDKREWHNIFKVLKXXXXTNQEY>PAKLSFRNEGEIKSFPDKQK

Parental  LKEFITKKPILQEMLK
          LKEFIT....L.E.LK
Retrocopy LKEFITTRLTL*EVLK

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	0.06 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_531 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_531 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_531 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,