RetrogeneDB ID: retro_ecab_1043

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: Un0077:24067..24941(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LCORL
• Ensembl ID: ENSECAG00000000648
• Aliases: None
• Description: ligand dependent nuclear receptor corepressor-like [Source:HGNC Symbol;Acc:30776]

Sequence

>retro_ecab_1043
TTGAAGGATTGTCTACCATCTCTTGATTCTTCACAGTCAACACCAACAGAGAAACTGTCATCTCAGGGCCAGTCCAACAC
TGAAAGACTGAATGCCAAGCAGAAAATTAGCTAAATGCACTCTTTCGAAAGAAAGACCTTCCTCAGAACTGTGATCCTAA
CATTCCCCTAGTTGCTCAGGAATTAATGAAAAAGATGATACGTCAGTTTGCAATTGAGTATATTTCAAAAAGTGGTAAAA
TTCAAGAGAATAGAAATGGTTCAATTGGACCAAGTCTAATATGTAAAAGTATTCAAATGAATCAAGCAGAAAACTCCCTT
CAGGAAGAACAGGAAGGCCCCTTAGACCTCACTGTGAATCGAATGCAAGAACAAAATACTCAGCAAGGGGATGGAGTGTT
AGATCTCTCTACAAAGAAAACCAGCATAAAATCTGAAGAGTCGTCCGTATGCGATCCTTCTTCTGAAATTCAATGGCTGG
GAGACTACAGAGAAACAGAGAGGACTATGTGGAGAGAAGTGCTGAGTTTGCAGATGGTTTGCTCTCAAAAGCTTTGAAAG
ACATTCAGTCTGGAGCACTGGACAGAAATAAAGCAGGCATACCTCAAAAAACTTTACTTCTCCACTTAGAAGCCTTACCA
GCAGGGAAGCCTGCATCTTTTAAAAACAAAGCTCGAGATTTCAGTGATAGTTACTCATATAAAGACAGTAAAGAAACTTG
TGCAGTGCTGCATAAAGTAGCCCTGTGGGCAAGAGCTCAAGCAGAGCGCACAGAAAAAAGTAAACTCAATCTAATTTAAA
GAAAAAAATGAAAGCCTACAATATGAAACTTCACGTCCTACTGTACAGTTAAAAATTCCTCAACTACGAGTAAG

Alignment

ORF - retro_ecab_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.95 %
• Parental protein coverage: 53.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSDCLPSLDSSQSTPTEELSSQGQSNTEKI-ECQAESYLNALFRKKDLPQNCDPNIPLVAQELMKKMIRQ
          ..DCLPSLDSSQSTPTE.LSSQGQSNTE...ECQAE..LNALFRKKDLPQNCDPNIPLVAQELMKKMIRQ
Retrocopy LKDCLPSLDSSQSTPTEKLSSQGQSNTERL<ECQAEN*LNALFRKKDLPQNCDPNIPLVAQELMKKMIRQ

Parental  FAIEYISKSGKIQENRNGSIGPSLICKSIQMNQAENSLQEEQEGPLDLTVNRMQEQNTQQGDGVLDLSTK
          FAIEYISKSGKIQENRNGSIGPSLICKSIQMNQAENSLQEEQEGPLDLTVNRMQEQNTQQGDGVLDLSTK
Retrocopy FAIEYISKSGKIQENRNGSIGPSLICKSIQMNQAENSLQEEQEGPLDLTVNRMQEQNTQQGDGVLDLSTK

Parental  KTSIKSEESSICDPSSE-NSVAGRLHRNREDYVERSAEFADGLLSKALKDIQSGALDINKAGILYGIPQK
          KTSIKSEESS.CDPSSE.NS.AGRL.RNREDYVERSAEFADGLLSKALKDIQSGALD.NKAGI....PQK
Retrocopy KTSIKSEESSVCDPSSE<NSMAGRLQRNREDYVERSAEFADGLLSKALKDIQSGALDRNKAGI----PQK

Parental  TLLLHLEALPAGKPASFKNKTRDFNDSYSYKDSKETCAVLQKVALWARAQAERTEKSKLNLLETSELKFP
          TLLLHLEALPAGKPASFKNK.RDF.DSYSYKDSKETCAVL.KVALWARAQAERTEKSKLNL......K.P
Retrocopy TLLLHLEALPAGKPASFKNKARDFSDSYSYKDSKETCAVLHKVALWARAQAERTEKSKLNLI*RKK*K-P

Parental  TASSYLHQLTLQKMVTQFK
          T........T.....T..K
Retrocopy TI*NFTSYCTVKNSSTTSK

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	2.36 RPM	1.36 RPM
SRP021940_cerebellum	2.29 RPM	0.93 RPM
SRP021940_embryo	7.54 RPM	3.84 RPM
SRP021940_placental_villous	2.69 RPM	1.49 RPM
SRP021940_synovial_membrane	3.82 RPM	1.51 RPM
SRP021940_testis	0.51 RPM	3.01 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1043 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1043 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000648	1 retrocopy	retro_ecab_1043 ,