RetrogeneDB ID: retro_ecab_343

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:1677925..1678870(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WASF1
• Ensembl ID: ENSECAG00000022222
• Aliases: None
• Description: WAS protein family, member 1 [Source:HGNC Symbol;Acc:12732]

Sequence

>retro_ecab_343
GATCATGTGGATGGATTTTATTTTCTTTCTGCCTTGACATTTAGTCAGATGAGTGAACTACAGCTGAGAAAAAATTCTTA
CCCAGACCACAAGAGTCATCTCCACTTCCACCAATGCATGGAACAGAAGCCGTGAAACCTATACCTACTTGTATCAGTTC
TGCTACAGGTTTGATAGAAATTTGCCTCAGTCACCAACCATGGTCAGAACTCCTATGTTTGTGAGTCCCACTCCCCACAC
ACTTTGTCCACCACTTCTTCCATCTCCCTTGTCAACTTCTTCATTAAACGCTTCAATGACTTCAACTCCTCGCCCACCAG
TACTTCCCCCGCCTCCAGCTCCAACTGCTGTTTTGCAAGCTGCAACAGTACCACCACCTCCAGCTCCTCTTCAGATTGTC
CCTGGAGTTCTCCATCCAACTCCTTCTCCAACTACACCTCCTCTAGTACAGCCTCTCTACCTGTTGCTAGACCTGTACTG
GTATGTGAGACTGTACCAGTTCATCCACTCCCACAAGCTGAAGTCCAGGGGCTGCTTTCACCTCCACCACCTCCCCCTCT
GCCTCCACCTCGCATTTGACCATCACCACCTGTCACAGTTACAGCTCTTTGTTCATCTTCCCTCTGGGCTATATCCAACA
ACACCTACTACTGCCCCAAGTGTCCATGTTCCATTAATGCCTCCATCTCCCCCATCACAAGTTATACCTGTTTCTGAGCC
AAAGTGTCACCAATCAATTATACTTGTAATCGGTGATGCCGAGAACGTATTTCTGGAACCAAAACAAAAGGTATTCAGCT
ATGCAAAGTAGAAGAGCAGTGTGGACAGGGAGCTAAACATGAACACATTAAAAATGATGTTGCCATCATCCTGTCCCCCT
GTATTGCTGTGGAACATAGTGATTCAGAAGATGATTCAGAATTTGATGAAGGAGATTAGTTGGAA

Alignment

ORF - retro_ecab_343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.28 %
• Parental protein coverage: 56.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DHMDGSYSLSALPFSQMSELLTRAEERVLVRPH-EPPPPPPMHGAGDAKPIPTCISSATGLIE-NRPQSP
          DH.DG.Y.LSAL.FSQMSEL..R.........H..P.PP..MHG....KPIPTCISSATGLIE.N.PQSP
Retrocopy DHVDGFYFLSALTFSQMSELQLRKNSYPDHKSH<SPLPP--MHGTEAVKPIPTCISSATGLIE<NLPQSP

Parental  ATGRTPVFVSPTPPP-PPPPLPSALSTSSLRASMTSTPPPPVPPPPPPPATALQAPAVPPPPAPLQIAPG
          ...RTP.FVSPTP....PP.LPS.LSTSSL.ASMTSTP.PPV.PPPP.P...LQA..VPPPPAPLQI.PG
Retrocopy TMVRTPMFVSPTPHTLCPPLLPSPLSTSSLNASMTSTPRPPVLPPPPAPTAVLQAATVPPPPAPLQIVPG

Parental  VLHPAPPPIAPPLVQP-SPPVARAAPVCETVPVHPLPQGEVQGLPPPPPPPPLPPPGIRPSSPVTVAAL-
          VLHP.P.P..PPLVQP.S.PVAR...VCETVPVHPLPQ.EVQGL..PPPPPPLPPP.I.PS.PVTV.AL.
Retrocopy VLHPTPSPTTPPLVQP<SLPVARPVLVCETVPVHPLPQAEVQGLLSPPPPPPLPPPRI*PSPPVTVTAL>

Parental  AHPPSGLHP-TPSTAPGPHVPLMPPSPPSQVIPASEPKRHPSTLPVISDARSVLLEAIR-KGIQLRKVEE
          .H.PSGL.P.TP.TAP..HVPLMPPSPPSQVIP.SEPK.H.S...VI.DA..V.LE....KGIQL.KVEE
Retrocopy VHLPSGLYPTTPTTAPSVHVPLMPPSPPSQVIPVSEPKCHQSIILVIGDAENVFLEPKQ<KGIQLCKVEE

Parental  QREQEAKHERIENDVATILSRRIAVEYSDSEDDSEFDEVDWLE
          Q..Q.AKHE.I.NDVA.ILS..IAVE.SDSEDDSEFDE.D.LE
Retrocopy QCGQGAKHEHIKNDVAIILSPCIAVEHSDSEDDSEFDEGD*LE

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	0.18 RPM
SRP021940_cerebellum	0.00 RPM	65.43 RPM
SRP021940_embryo	0.00 RPM	49.07 RPM
SRP021940_placental_villous	0.00 RPM	6.45 RPM
SRP021940_synovial_membrane	0.00 RPM	4.78 RPM
SRP021940_testis	0.00 RPM	110.17 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_343 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_343 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000022222	1 retrocopy	retro_ecab_343 ,
Otolemur garnettii	ENSOGAG00000008623	1 retrocopy	retro_ogar_895,
Ictidomys tridecemlineatus	ENSSTOG00000005949	1 retrocopy	retro_itri_1319,