RetrogeneDB ID: retro_ecab_1013

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 9:63065600..63066380(+)
• Located in intron of: ENSECAG00000009462

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIX1
• Ensembl ID: ENSECAG00000021643
• Aliases: None
• Description: Lix1 homolog (chicken) [Source:HGNC Symbol;Acc:18581]

Sequence

>retro_ecab_1013
AGAGACCTGGGGCTCAGTTCCAAAGACTTGAATGGTGTGTCTGTGTTAACAGGAACTTTGGGAAAGCAAGCAGCAGCAAA
GGGCTGCTTTCCCAAGTGGAGCCATGGTGGTCTACAAGTCCACGCCATCTCTTGGGCCTCCCTCTGTGAGTGATGTGACC
TTCCAGGGGGGACAGTATTTTGGCAACTTTCAGTGCTGCTTCACTAGAGCTGAGGCATGACAGGATACAGCTAAAGTGGT
CTGGGTCAACTCCTTTTTCAATAAGCTGCCCTCTCCAAGGATCACCAAGGAATTCATCAAAGGAAGTGTTCAGGAAGCAA
TTGCCTATGCCAGCAACACTCTAGACTTGCTTATGACCCCAGCATCAGCATCAGAGCCCATCATGTTCGAGTCAAATATA
GGGAAGACCATATTTGGAATTCCAGGAGCCAATGACCATTTTCCAACTATCGCACTGGAAGGGAAGCCTTAAAAGCCCTT
CGTGAAACAAAGTGTTCCCAACAGAAAATCTTCTCCCACTATTTCCAGTATGCCCTAGATGAAAAGATGCGCAGCTGTGT
GGCCCTGGACTGGATTATAAAGGAGTAAGAGTTACCAGGAATGCTCTCTGAAGAGCAATGAGTGGTCTTGAGGGAGTTAG
AGCAAGCCAGGAAAGCAGGATAACCATACTGCTACATAGAAAATAAAGAAATTTGGAGCTTAGCCTTGACTTAGATCCAC
AGTGGGCTTGACACTTCCTCGCCCAGTGATGATCTGCTGAGCCACACGACTCTGTGCGGC

Alignment

ORF - retro_ecab_1013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.77 %
• Parental protein coverage: 92.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RDPALVFKDLNVVSML-QEFWESKQE-RAAFPSEGVVIYESLPSPGPPFVSYVTLPGGSCFGNFQCCLSR
          RD..L..KDLN.VS.L.QE.WESKQ..RAAFPS...V.Y.S.PS.GPP.VS.VT..GG..FGNFQCC..R
Retrocopy RDLGLSSKDLNGVSVL>QELWESKQQQRAAFPSGAMVVYKSTPSLGPPSVSDVTFQGGQYFGNFQCCFTR

Parental  AEARRDAAKVALINSLFNELPSRRITKEFIMESVQEAVASTSGTLDDADDPSTSIGAYHYMLESNMGKTM
          AEA..D.AKV...NS.FN.LPS.RITKEFI..SVQEA.A..S.TLD....P.........M.ESN.GKT.
Retrocopy AEA*QDTAKVVWVNSFFNKLPSPRITKEFIKGSVQEAIAYASNTLDLLMTPASA--SEPIMFESNIGKTI

Parental  -LEFQELMTIFQLLHWNGS-LKALRETKCSRQEVISYYSQYSLDEKMRSHMALDWIMKERESPGILSQEL
          .LEFQE.MTIFQL.HW.GS.LKALRETKCS.Q...S.Y.QY.LDEKMRS..ALDWI.KE.E.PG.LS.E.
Retrocopy >LEFQEPMTIFQLSHWKGS>LKALRETKCSQQKIFSHYFQYALDEKMRSCVALDWIIKE*ELPGMLSEEQ

Parental  RMALRELEEARKAGQELRFYKEKKEILSLALTQIYSESDTSSPSDDQLSLTALCG
          ...LRELE.ARKAG.......E.KEI.SLALT.I.S..DTSSPSDD.LS.T.LCG
Retrocopy *VVLRELEQARKAG*PYCYI-ENKEIWSLALT*IHSGLDTSSPSDDLLSHTTLCG

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	0.47 RPM
SRP021940_embryo	0.00 RPM	25.11 RPM
SRP021940_placental_villous	0.00 RPM	0.05 RPM
SRP021940_synovial_membrane	0.00 RPM	0.66 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_1013 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1013 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
Dasypus novemcinctus	ENSDNOG00000012335	1 retrocopy	retro_dnov_2085,
Equus caballus	ENSECAG00000021643	1 retrocopy	retro_ecab_1013 ,
Mus musculus	ENSMUSG00000047786	1 retrocopy	retro_mmus_448,