RetrogeneDB ID: retro_ecab_642

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 25:6834234..6835037(+)
• Located in intron of: ENSECAG00000018297

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000016527
• Aliases: None
• Description: None

Sequence

>retro_ecab_642
GAGATAAACAATCTACCTGATAAACAGTAAAAACTACTAGTCATAAGGATGCTCAATGATCTTAGGAGAAGAACAGATGA
ACACAATGAGAATTTTAACAAAGACTTGGAAAATATAAAAAAGAACCAATCAGAACTGAAGTATAATGGAAATGAAAAAT
TCACTAGAGGGAATCAACAGTACAGTATATGACACAGAACAGATCAGCAATCTGGATGAAAGAGTAGAGGAAATCACTCA
AGCTAAACAGAAAAAAGAAAAAAGGATTAAAAGGAAAGAGGACAGTCTAAGGGACCTCTGGGACAACAGTAAGTGTACTA
AATCTGTATTATAGGTGTCCCAGAAGGAGATGAGAGACAAAGGGGCAGAGAACTTATTTGAAGAAATAATAGCCAAAAAC
TTCCCTAACTGGGGAAGGAAATGGACATCCAGGTACAGGAAACACGGAGCACCAAACAAGATGAACCCAAAGAGGCCCAC
ATCAAGATACATTATAATTAAAATGTCAAGAATTAAAGATAAACAGAGAATGCTAAAAGCTGCAAAAGAAAAGCAAAAAG
TTACATACAAAGGAAACCCCCCAGGCTATCAGCTGACTTCTCAGCAGAAACCTTACAGGATAGCAGGGAGTGACATGATA
TATTCCAAGTGCTGAGAGGAAAAAGACCTACAGCCAAGAATACTCTAATTGGCAAGGCAATCATTCAGAATGGAAGGAGA
GAGAGAGTTTTCCAGATGAGCAAAAACTAAAGGAATTCGTCACTACTAAACCAGCCTTACAAGAAAGGTTAAAGGGACTT
ATT

Alignment

ORF - retro_ecab_642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.61 %
• Parental protein coverage: 98.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EINNLPDKEFKQKVIRMLTDLGRRMDEPSGNFNKELENIKKNQSKNKHRLKQKTTHQLGKNICKDSI-AQ
          EINNLPDK..K..VIRML.DL.RR.DE...NFNK.LENIK....KN...LK..............SI...
Retrocopy EINNLPDKQ*KLLVIRMLNDLRRRTDEHNENFNKDLENIK----KNQSELKYNGNEKFTRGNQQYSI>DT

Parental  ERTNKLDKRLEEITQADQIKEKRIKKNEDGLRDLWNNIKHTNIHIIDVPEGEERDKGAENLFGEIIAENF
          E....LD.R.EEITQ............ED.LRDLW.N.K.T......V...E.RDKGAENLF.EIIA.NF
Retrocopy EQISNLDERVEEITQXXXXXXXXXXXXEDSLRDLWDNSKCTK-SVL*VSQKEMRDKGAENLFEEIIAKNF

Parental  PNLRRKYPGEAQR--APNKINPKRPTPRHIIIKMSKSKDKERILNALRERQQVTYKGNPI-RLSANFSAE
          PN..RK.........APNK.NPKRPT.R.IIIKMS..KDK.R.L.A..E.Q.VTYKGNP..RLSA.FSAE
Retrocopy PNWGRKWTSRYRKHGAPNKMNPKRPTSRYIIIKMSRIKDKQRMLKAAKEKQKVTYKGNPP<RLSADFSAE

Parental  TLETRREWHDILKVLKGK-NLQPRILYSARLSF-MEGEIEF-PDKQNLEEFITKKPALQEMLNGLI
          TL...RE.HDI..VL.GK..LQPRIL..AR.SF.MEGE.EF.PD.Q.L.EF.T.KPALQE.L.GLI
Retrocopy TLQDSRE*HDIFQVLRGK>DLQPRIL*LARQSFRMEGEREF>PDEQKLKEFVTTKPALQERLKGLI

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	0.05 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.08 RPM	0.00 RPM
SRP021940_testis	0.06 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_642 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_642 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_642 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,