RetrogeneDB ID: retro_ecab_714

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:39219756..39220578(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000022782
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000023806
• Aliases: None
• Description: None

Sequence

>retro_ecab_714
AGGAGACAAAGGAATATGTTCCAAATAAGGGAACAGGACAGTTCCTCAGAAAAAGAGCTAAACAAAACAGAGATAAACAA
TCTACTTGATAAAGAGTACAAACTAATACTCATAAGGATGCTTACTGATCTGGGGAGAAGAATAGATGAACACAGTGAGA
ACTTCAACAAAGAACTAGAAAATATGAAAAAGAACCAATCAGAGCTGAAGAATACAATAATGGAAATGAAAATTTCACTT
GAGGGAATCAACAGCAGAGTAGATGACACAGAAGAACTGATCAGCCATCTGGATGACAGAGTAGAGGAAATAGCCTAAGC
TGAACAGAAAAAAAGAAAAAAGAATTAAAAAAAATGAGGACAGTCTAAGGGACCTCTGGGACAACATCAAATGTATTAAC
ACCTGCATTATAAATGTCCCAGAAGGAAAAGAGAAAGACAAGGGGCACAGAACTTATTTGAAGAAATAATACCTGAAAAC
TTCCGTAACCTGAGAAAGGAAACAGATATCCAGGTACTGGAAACACCGAAAGCACCACACAAGATGAATCCAAAGAGGCC
CACACCAAGACACATTATAATAAAAATGTCAAGAATTAAAGATAAGGAGAGAATCCTAAAAGCTGCAAGAGACAAGCAAT
AAGTTACATACAAAACCCCCCATAAATCTATAAGCTGACTTTTCAGCAGAAACTTTACAGGCTAGAAGGGAGTGGCACTA
TATACTCAAAGTGATGAAAGAAAAAACCTACCATCAAGAATACTGTACCTGGCAAGGTTATCATTCAGAATTGAAGGAGA
GATAAAGAGATTTACAGATGAG

Alignment

ORF - retro_ecab_714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.78 %
• Parental protein coverage: 97.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RRQRNMFHARVQDKTPEKELNETQRDNLPDKEFKQKGIRMLIDLGRRMDKHSENVNKELENIKKSQSEMK
          RRQRNMF..R.QD...EKELN.T...NL.DKE.K...IRML.DLGRR.D.HSEN.NKELEN.KK.QSE.K
Retrocopy RRQRNMFQIREQDSSSEKELNKTEINNLLDKEYKLILIRMLTDLGRRIDEHSENFNKELENMKKNQSELK

Parental  STILKMKNSLEGLNSRVDDTEEWIKKLDEKLEEIS-QVNQVKEKTILKNDSKIKELWDNIKHANIRIISV
          .TI..MK.SLEG.NSRVDDTEE.I..LD...EEI....N................LWDNIK..N..II.V
Retrocopy NTIMEMKISLEGINSRVDDTEELISHLDDRVEEIA>KLNXXXXXXXXXXEDSLRDLWDNIKCINTCIINV

Parental  PGGEERHKGE-ENLFEEIIDENFPNLRKETDIQVQEEQRAPNKSSPKRPTPIHIII-KMSKIKDKERILK
          P.G.E..KG...NLFEEII.ENF.NLRKETDIQV.E...AP.K..PKRPTP.HIII.K....K......K
Retrocopy PEGKEKDKGH<QNLFEEIIPENFRNLRKETDIQVLETPKAPHKMNPKRPTPRHIII>KCQELKIRRES*K

Parental  AARERPEVTYKGKPIRLSADFSAETLQATREWHDIFKVLKGK-NLQPRIFYPSRSSFRMEGEIKRFPDK
          ...E.........PI.L.ADFSAETLQA.REWH.I.KV.K.K.NL..RI.Y..R.SFR.EGEIKRF.D.
Retrocopy L-QETSNKLHTKPPINL*ADFSAETLQARREWHYILKVMKEK<NLPSRILYLARLSFRIEGEIKRFTDE

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	0.12 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.28 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.08 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_714 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_714 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010030	21 retrocopies	retro_ecab_1021, retro_ecab_1023, retro_ecab_1035, retro_ecab_1071, retro_ecab_1089, retro_ecab_136, retro_ecab_182, retro_ecab_201, retro_ecab_281, retro_ecab_306, retro_ecab_486, retro_ecab_521, retro_ecab_537, retro_ecab_582, retro_ecab_590, retro_ecab_658, retro_ecab_670, retro_ecab_722, retro_ecab_786, retro_ecab_974, retro_ecab_996,
Equus caballus	ENSECAG00000016527	5 retrocopies	retro_ecab_214, retro_ecab_642, retro_ecab_879, retro_ecab_888, retro_ecab_993,
Equus caballus	ENSECAG00000020332	9 retrocopies	retro_ecab_1018, retro_ecab_117, retro_ecab_125, retro_ecab_346, retro_ecab_54, retro_ecab_604, retro_ecab_774, retro_ecab_775, retro_ecab_878,
Equus caballus	ENSECAG00000022034	4 retrocopies	retro_ecab_1039, retro_ecab_278, retro_ecab_821, retro_ecab_858,
Equus caballus	ENSECAG00000023806	15 retrocopies	retro_ecab_1040, retro_ecab_1050, retro_ecab_1073, retro_ecab_1077, retro_ecab_1108, retro_ecab_176, retro_ecab_241, retro_ecab_298, retro_ecab_339, retro_ecab_714 , retro_ecab_778, retro_ecab_781, retro_ecab_852, retro_ecab_855, retro_ecab_953,