RetrogeneDB ID: retro_ecab_575

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:26211664..26213090(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000013114
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACCSL
• Ensembl ID: ENSECAG00000011908
• Aliases: None
• Description: 1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like [Source:HGNC Symbol;Acc:34391]

Sequence

>retro_ecab_575
GACCTGGTGCTGGAAGAGGAGAGTCAGAACCAGGCCACTCAAGAGCAGGAAGCCCTCTTGGACCACCTAATGTGCCAGAT
GGTCAATCTGCTACAGTCTGGGACCACAGGTGGCCTGGGGATCCAACTATCTTGTCCTTCCCTAGACTCTAAGGGTGATG
TCAGTGGTGGGCAGTGGGCTCAGTCATGCAGGCAGCCTAGGCAGCTTGTTCACCAACTGAGTGATTTTGAAGCTGCATTT
GTCAGCTGTGACCTGTCCAATCATGGGATTGATATCTCTCCCTTACACCACTCCAGCTTTCAGGACTACATTACCTACCA
AGGAGGCAAATACCACGAGGACAAGAACACCCTGGCTTCATTAACCTTGGTTCCAGTGAGAATACGCTCTGCATTGATCT
GGTGACTTCCGGTTGAGTCAGAGTGACATGAACCGCATTGAGGAGATCCCACTGTAAGATCCCGATTAGAGAGGGCAACT
GTTCCTGCAGGAAGAAGCGTCTCAGTTCCTGACCTCTTGCTGCAAGGCTCCTGCTTATCTCGATCCAGAAAACTCGGTTG
TTCTAAATGGCCGCTGCTCTGTCTTCTCTGTGCTGGCCATGGTTCTGTGTGATCCAGGTGAGGCCTTCCTGATTCCCATC
CCCTTTCATGGTGGCTTTGTCGTTAGATCCCTCCTGCATGCGAAAGTTGAGCTGATTCTTGTCTACCTGGACAGTGAGAT
CACTGATCCGAACATCTGTGCTTTCCAGCTTGCTGTGGGCAAGTTGAAGCAAGCCCTGCCGAAGGCTGGGCTTAAGGGGA
AAAAGGTAGGGGACCTCAGGCTAATTCACTCTCAGAATCCTCCGGGTGACATCTACTTCCAAGACTCATTGAAGGAATAC
CTGGAATTTGCCAAGAGGTATAACCTACATGTGATTATAGATGAGAGGTATGTGTTATCTATGTTGGATGAATCTGTCGT
ATTCCACAGAGTTCTGAGCTGAAAGTTTACTGACCCCAACAGGACCCACGTGATCTGGTGTACCAGTAAGGATTTTGCAT
CTCTAGCTTCTGCTTTGGCACTCTGTATACCCACAATAAGGCGATGGTCTCTGCCGTGAGCTCCTTTGGCCACCTCCGCA
GAATGTCTGGCATCACCCAGCTTGAACTGTGTTGCTGTTCCTGGACAGAGAATGGATTGACGAAGTGCATCTGACCACTA
ATCGCTCCCAGCTGCAGGCAGCTCACAGGTACATCATTAACAAGTCGAAGCTTTGGAGATCCCCTTTCTCAATCGTGTCT
CTGGCCTCAGTGTCTGGATTAACTTGAAAAAGTACCTGGACTCATGCACATTTGAGAAGGAGCTGCTTTCCCATTGCTGA
TTCCTGGACAACAAGCTGGTGCTGTCTCATGGTAAGACCTATAAATGTAAGGAGCCTGGCTGGTTC

Alignment

ORF - retro_ecab_575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 83.75 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DLPLEEQRHNQATGEQEAF----LRRVVNLLQSGAMWGLGLQAPRPTLGPRDDAGGGQQAQLSRQLDQLV
          DL.LEE...NQAT.EQEA.........VNLLQSG...GLG.Q...P.L....D..GGQ.AQ..RQ..QLV
Retrocopy DLVLEEESQNQATQEQEALLDHLMCQMVNLLQSGTTGGLGIQLSCPSLDSKGDVSGGQWAQSCRQPRQLV

Parental  HQLSHLEVAFVSHDLSNRGIDISAFERSKFQDFKTYQGDKYHEDKNTM-GFINLGVSENKLCTDLMTE-R
          HQLS..E.AFVS.DLSN.GIDIS....S.FQD..TYQG.KYHEDKNT..GFINLG.SEN.LC.DL.T..R
Retrocopy HQLSDFEAAFVSCDLSNHGIDISPLHHSSFQDYITYQGGKYHEDKNTL<GFINLGSSENTLCIDLVTS<R

Parental  LSRSDMNHLEDALLQYSDQRGQPFLREEVARFLTYYCKSPARLDPENVVVLSGCCSVFSALATVLCDPGE
          LS.SDMN..E...L...D.RGQ.FL.EE...FLT..CK.PA.LDPEN.VVL.G.CSVFS.LA.VLCDPGE
Retrocopy LSQSDMNRIEEIPL*DPD*RGQLFLQEEASQFLTSCCKAPAYLDPENSVVLNGRCSVFSVLAMVLCDPGE

Parental  ALLTPTPFFGGLVMGSYLYSKVELMPVHLDSEITDGSARPFQLTVDKLEQALLEATLKGKKVRGLLLINP
          A.L.P.PF.GG.V..S.L..KVEL..V.LDSEITD.....FQL.V.KL.QAL..A.LKGKKV..L.LI..
Retrocopy AFLIPIPFHGGFVVRSLLHAKVELILVYLDSEITDPNICAFQLAVGKLKQALPKAGLKGKKVGDLRLIHS

Parental  QNPLGDVYSRDSLEEYLEFAKRYNLHVIIDELYMLSVFDDSVTFHSVLSMESLPDPNRTHMIWGTSKDFG
          QNP.GD.Y..DSL.EYLEFAKRYNLHVIIDE.Y.LS..D.SV.FH.VLS.....DPNRTH.IW.TSKDF.
Retrocopy QNPPGDIYFQDSLKEYLEFAKRYNLHVIIDERYVLSMLDESVVFHRVLS*K-FTDPNRTHVIWCTSKDFA

Parental  -ISGFRFGALYTHNKEVASAVSSFGFLNGISGITQYKLC-RLLQDREWIDKVYLPTNHSRLKAAHRYITN
          .IS.F.FG.LYTHNK...SAVSSFG.L...SGITQ..LC..L..DREWID.V.L.TN.S.L.AAHRYI.N
Retrocopy <ISSFCFGTLYTHNKAMVSAVSSFGHLRRMSGITQLELC<LLFLDREWIDEVHLTTNRSQLQAAHRYIIN

Parental  KLK-ALKIPFLNRGSGLYVWMNLKEYLQPCTFEEELLLHHRFLGNKLILSPGKTYMCKEPGWF
          K.K.AL.IPFLNR.SGL.VW.NLK.YL..CTFE.ELL.H..FL.NKL.LS.GKTY.CKEPGWF
Retrocopy KSK<ALEIPFLNRVSGLSVWINLKKYLDSCTFEKELLSHC*FLDNKLVLSHGKTYKCKEPGWF

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	0.00 RPM	0.10 RPM
SRP021940_placental_villous	0.00 RPM	27.47 RPM
SRP021940_synovial_membrane	0.11 RPM	0.05 RPM
SRP021940_testis	0.00 RPM	0.13 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_575 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_575 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011384	1 retrocopy	retro_cjac_100,
Dipodomys ordii	ENSDORG00000005058	1 retrocopy	retro_dord_340,
Equus caballus	ENSECAG00000011908	1 retrocopy	retro_ecab_575 ,
Echinops telfairi	ENSETEG00000009026	2 retrocopies	retro_etel_1006, retro_etel_204,
Homo sapiens	ENSG00000205126	1 retrocopy	retro_hsap_3553,
Myotis lucifugus	ENSMLUG00000005151	1 retrocopy	retro_mluc_1235,
Nomascus leucogenys	ENSNLEG00000017966	1 retrocopy	retro_nleu_2326,
Ochotona princeps	ENSOPRG00000002097	1 retrocopy	retro_opri_526,
Ochotona princeps	ENSOPRG00000006805	7 retrocopies	retro_opri_1064, retro_opri_1151, retro_opri_251, retro_opri_252, retro_opri_398, retro_opri_399, retro_opri_808,
Pongo abelii	ENSPPYG00000003340	1 retrocopy	retro_pabe_2934,
Pan troglodytes	ENSPTRG00000028662	1 retrocopy	retro_ptro_2414,
Tupaia belangeri	ENSTBEG00000016623	1 retrocopy	retro_tbel_3677,
Tursiops truncatus	ENSTTRG00000002727	1 retrocopy	retro_ttru_1321,