RetrogeneDB ID: retro_ecab_387

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:69686796..69687506(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000012757
• Aliases: None
• Description: None

Sequence

>retro_ecab_387
ATTAATGAACAGAAGGAATACTTCACCAAAGAGATTGAAGCTCTAAAAAAAACCCAAACAAATTCTGGATATGAAGAACA
TAATGAGATAAAAAATAATTTAGAAAGCATTAAAAATAGAGTAGACCTTTTGGAGGAGAGAATTAGTGAGTTCAAAGATG
AAAACCTAGAAATGATTCAGGTGGAGGAGAACTAAAATTTTTAAAAATGAAGAAATTCCTGACTCAATTAGGAGAAGTAA
CATAAGGACTATAGGTATCCCAGAGGGAGAAGTGAGAGAGAAAGGAGCAGAGAGCTTATTGAAAGAAATAATAGCTGAGA
ACTTCCCAAACCTGAGGATGGGACTGGACATGTAAGTACGTGAAGCTAACATAACTCCTAATTATGTCAATGCAAAAAGA
CCTTCTCCAAGGCGTATAATACTGTCAAAAGTCAATGACAAAGGAAAGATATGAAGGGCGGCAAGAGAGAAGAAAAACAT
ACAAAGGAACCAGCATCAGGCTTACAGCAGACTTCTCAACAGAAACCTTACAGGCTAAGAGACAGTGGAATAATATATTC
AAAATACTGAAAGACAAAAACTATCAACCAAGAATACTCTATCCACCAAAATTATCCTTCAGATATGACAGAGAAATAAA
GGAGAAACAAAAGCTGAGGGAGTTCATCAGCATTAGACCTGCCCTACAAGAAATGTTGAAGGGAGCCCTC

Alignment

ORF - retro_ecab_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.39 %
• Parental protein coverage: 90.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDELSENFKKELE--NKKRTNQKKTTILEIKNSLEGLNGRVDDTEEWISELDERLEEITQASQIKE-TRI
          ..E..E.F.KE.E......TN.......EIKN.LE....RVD..EE.ISE......E.....Q..E.T.I
Retrocopy INEQKEYFTKEIEAXXXXQTNSGYEEHNEIKNNLESIKNRVDLLEERISEFKD---ENLEMIQVEE>TKI

Parental  IKNTNMVKELWDNIKHNNIRLVGVPEGAERDKGAENLFEEVIAENFPNLRKETDWKTKKANRSPNFTNVK
          .KN.....E..D.I...NIR..G.PEG..R.KGAE.L..E.IAENFPNLR...D.....AN..PN..N.K
Retrocopy FKN----EEIPDSIRRSNIRTIGIPEGEVREKGAESLLKEIIAENFPNLRMGLDM*VREANITPNYVNAK

Parental  RPTPRHIVVKLAKVND-KEKILRAARQNKITYKGTSIRLSENFSADTLQARREWNDIFRTLKDKNLQPRI
          RP.PR.I...L.KVND.KE...........TYKGTSIRL...FS..TLQA.R.WN.IF..LKDKN.QPRI
Retrocopy RPSPRRII--LSKVND>KERY-EGRQERRKTYKGTSIRLTADFSTETLQAKRQWNNIFKILKDKNYQPRI

Parental  LYAVKISFKYDGEIKTFQDKQKLREFIATRPPLQEMLRKTL
          LY..K.SF.YD.EIK....KQKLREFI..RP.LQEML...L
Retrocopy LYPPKLSFRYDREIK---EKQKLREFISIRPALQEMLKGAL

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	0.03 RPM	0.10 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_387 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_387 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012757	4 retrocopies	retro_ecab_1053, retro_ecab_387 , retro_ecab_602, retro_ecab_990,