RetrogeneDB ID:

retro_ecab_424

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:17:62207472..62208055(-)
Located in intron of:ENSECAG00000019744
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSECAG00000018840
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ecab_424
TTAGAGGACAGGAATCTAGAAATGCTTCAGGTGCAGGGGGAGAGAAAACTAAGATTTTAAAAAAATGAAGAAATTCTTCA
AGAAATATCTGACTCAATTAGGAAAAGCAACATAAGGATTATAGGTATTCCAGAGGGAGAAAGGAGCAGGGAGTTTCTTT
AAAAAAAACAATAGCTGACAACTTCCCAAACCTCAGAAAGAATTGGACTTACAAGTATATGAAGCCAATGGAACCCCCAA
TTACATCAATGCAAAAAGACCTTCTCCAAGGCATATAATATTAAAACCGGCAAAAAGCAATGACAAAGAAAAATTACTAA
GGGCAGCAAGGCAGAAGTAAATAATCTACAAAGGAACCCCTATAAGGCTTTTAGCGGATTTCTCAGCAGAAACCTTAAGG
CTAAGAAGATGGAATCATATGTCCAAAATACTGAAAGCCAAAAACTTTCAGTCAAGAATACCTTATCCAGTGAAACTATC
CTTCATATACAATTGAGAAATGCAAGGTTTTCCAGATAAACAAAAGCTGAGAGAGTTCATTGACACAAGGCCTGCTTTAC
AAGAAATGACCAAGGACGTCCTC

ORF - retro_ecab_424 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.21 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLEDRNTEMLKMEEERELRLKRSEDIFQEIYNPIRKRNIRIISIPTGEERQNRRESLFKE-IITENFLNLG
LEDRN.EML....ER.LR....E.I.QEI...IRK.NIRII.IP...E....RE.L.....I..NF.NL.
RetrocopyLEDRNLEMLQVQGERKLRF*KNEEILQEISDSIRKSNIRIIGIP---EGERSREFLXXX<XIADNFPNLR
ParentalKG-LEIQVKEANRTPNYINVERPSPRHILVKLAKLVMKEYIMAEAARQKKITYKGSPIRLSADFSQTVQT
K..L..QV.EAN.TPNYIN..RPSPRHI..K.AK...KE.....AARQK.I.YKG.PIRL.ADFS.....
RetrocopyKN<LDLQVYEANGTPNYINAKRPSPRHIILKPAKSNDKEKLL-RAARQK*IIYKGTPIRLLADFSAETLR
ParentalRREWNDIIKILKYKNYPPRILYPVKLSFRYGREIKAFQDKQKLREFITTRPPLQEMMKTAL
.R.WN...KILK.KN...RI.YPVKLSF.Y..E...F.DKQKLREFI.TRP.LQEM.K..L
RetrocopyLRRWNHMSKILKAKNFQSRIPYPVKLSFIYN*EMQGFPDKQKLREFIDTRPALQEMTKDVL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 .03 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 - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_424 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_424 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_424 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG00000018840 28 retrocopies
retro_ecab_1000, retro_ecab_1011, retro_ecab_1045, retro_ecab_1062, retro_ecab_1076, retro_ecab_221, retro_ecab_243, retro_ecab_296, retro_ecab_322, retro_ecab_327, retro_ecab_424 , retro_ecab_482, retro_ecab_498, retro_ecab_523, retro_ecab_545, retro_ecab_564, retro_ecab_571, retro_ecab_663, retro_ecab_718, retro_ecab_742, retro_ecab_763, retro_ecab_787, retro_ecab_790, retro_ecab_824, retro_ecab_902, retro_ecab_908, retro_ecab_928, retro_ecab_929,


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