RetrogeneDB ID: retro_ecab_724

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:69573864..69575063(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAD1L1
• Ensembl ID: ENSECAG00000014242
• Aliases: None
• Description: MAD1 mitotic arrest deficient-like 1 (yeast) [Source:HGNC Symbol;Acc:6762]

Sequence

>retro_ecab_724
GAAGACCTAGGGGAAAACACCACCATCCTAACCATCCTGAGGTCTTTGAACAGCTTCATTTCTGAGTGAGTAGAGGGAGG
GTCTGGATTGGGTGTTTCCATCTCTGTGCAAGTTTCTCTGCAGATGCAGTACCAGCAGAGCATGCAGTTGGAGGAACCAG
CAGAACAGATCCATTCAGTCTCACCTCACCCAGACAGAGCTGGAAAAGATGCAGATGGAGCTGAGTCACAAGAGGGCTTA
AGTGGGGCTGGAGCAAGTGGCTAGCACCAGTGCTAGGAGCTAAGAACATGAGGTTTACTGCAACCAAGAGCCCTTGATGT
GCATTCTGCAGCTTCAGGAGCAGGAGGCTCAGATGGAGGATATTAAGAAGAAGCAGGCAGAGCACAGCAGGTTGTTTAAG
CAGCAGCTGGATGCTGCCAGCAAGAAGCTGCAAGAGAAGGAGGACCACTCAGCTGAAGCCTAAGAAACCATTAGTTTGTC
AAAGGGGAAGATATGGGAATCACAGTGGAATGTGATGAATGCGGAGATGCAGGTGAAGAGCCTGGAGTCTGACAAGCAGG
AGCTGGAGGAGCAGATGGACTTGCAGCACAAAAAAAAATGCCAGGAAGCTAATCAAAAATTCAGGAACTCCAAGCCAGTC
AAGAAGTGAGGGCAAACCAGGAACAGAGGATTAAGGATTTGAAGCAGAAGCTGTCCTTGCAGGAACAGGATGCTGCCATT
GTGAAGAACATGAAGTCTGAGCTGGTGCAGCTGCCCGAGAGGGAGAGGGAGCTGAACCATCTGAGGGAGGAGAACCTGCG
GAGATGTGAGAGACCGACAGGCTGCTCAGGGAAGAACTGGAGGGCCTGCAGGGGTGTTAGGAGAAGATGCAGGGAAATCT
CATTGACCTGGAGCTGGAGAAGACTACTGGAGAAGCTGCAAAGCTGGAAGGGACGGGAGCAGATCACAGGCTTGAACATT
AGGACCCTGAAGACCTTTCCAGTTTCATTGTCCAACTGCAGCAGAGAGAGCTTGCCCTGAAGGAAGGGAGCAGCTGCAGC
ACCAGCAGCCCCCCCGGGCCTGGAGAAGTTTAGGCAGCAGCTCCAGGAGGAAGTCTACCAGGTCTGCAGTCAGCTGCTGG
AGGGGAGGAAGAAGCGGAAGACCCACGAGGACCTGGCCTGAGACTTCAGAAACGGGTCCTGCTGCTGAAAAAGGTGAGA

Alignment

ORF - retro_ecab_724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.27 %
• Parental protein coverage: 56.29 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  EDLGENTTVLSTLRSLNNFISQRVEGGSGLDVSTSAQGSLQMQYQQSMQLEE-RAEQIRS-KSHLIQMER
          EDLGENTT.L..LRSLN.FIS..VEGGSGL.VS.S.Q.S...Q.Q........R..Q.RS..SHL.Q.E.
Retrocopy EDLGENTTILTILRSLNSFISE*VEGGSGLGVSISVQVS--LQMQYQQSMQL>RNQQNRSIQSHLTQTEL

Parental  EKMQMELSHKRARVELERAASTSARSYEREVDRNQELLTRIRQLQEREAEVEEKMKEQQERSRLCKQSLD
          EKMQMELSHKRA.V.LE..ASTSARS.E.EV..NQE.L..I.QLQE.EA..E...K.Q.E.SRL.KQ.LD
Retrocopy EKMQMELSHKRA*VGLEQVASTSARS*EHEVYCNQEPLMCILQLQEQEAQMEDIKKKQAEHSRLFKQQLD

Parental  VASKKLREKEDGLAEAGETISALKGRVSELQWSVMNQEMQVRSLESEKQELKEQLDLQHKKW-QEANQK-
          .ASKKL.EKED..AEA.ETIS..KG...E.QW.VMN.EMQV.SLES.KQEL.EQ.DLQH....QEANQK.
Retrocopy AASKKLQEKEDHSAEA*ETISLSKGKIWESQWNVMNAEMQVKSLESDKQELEEQMDLQHXXXCQEANQK<

Parental  IQELQASQEVRADQEQRIKDLEQKLSLQEQDAVIVKNMKSELVRLPKMERELKQLREENVHLR-EMRETN
          IQELQASQEVRA.QEQRIKDL.QKLSLQEQDA.IVKNMKSELV.LP..EREL..LREE...LR.EM.ET.
Retrocopy IQELQASQEVRANQEQRIKDLKQKLSLQEQDAAIVKNMKSELVQLPERERELNHLREE--NLR<EM*ETD

Parental  GLLREELEGLRRKLGRQEKMQENLVDLELEKE-RLLAKLQSWERLDQTTGLSIRT-PEDLSRFIVELQQR
          .LLREELEGL....G..EKMQ.NL.D..LE.E.RLL.KLQSW....Q.TGL.IRT.PEDLS.FIV.LQQR
Retrocopy RLLREELEGLQ---GC*EKMQGNLID--LELE>RLLEKLQSWKGREQITGLNIRT<PEDLSSFIVQLQQR

Parental  ELALKDRNSSITCS-ARGLEKVRQQLQEEVRQVSSQLLEERKRRETHEALA-RRLQKRVLLLTKER
          ELALK...S..T.S...GLEK.RQQLQEEV.QV.SQLLE.RK.R.THE.LA..RLQKRVLLL.K.R
Retrocopy ELALKEGSSCSTSS>PPGLEKFRQQLQEEVYQVCSQLLEGRKKRKTHEDLA<LRLQKRVLLLKKVR

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	18.54 RPM
SRP021940_cerebellum	0.00 RPM	28.10 RPM
SRP021940_embryo	0.00 RPM	46.31 RPM
SRP021940_placental_villous	0.00 RPM	13.09 RPM
SRP021940_synovial_membrane	0.00 RPM	25.34 RPM
SRP021940_testis	0.00 RPM	68.48 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_724 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_724 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_724 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000014242	1 retrocopy	retro_ecab_724 ,
Latimeria chalumnae	ENSLACG00000017346	17 retrocopies	retro_lcha_102, retro_lcha_106, retro_lcha_109, retro_lcha_113, retro_lcha_114, retro_lcha_115, retro_lcha_33, retro_lcha_36, retro_lcha_41, retro_lcha_44, retro_lcha_60, retro_lcha_66, retro_lcha_70, retro_lcha_79, retro_lcha_80, retro_lcha_93, retro_lcha_99,