RetrogeneDB ID: retro_ecab_944

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:4145055..4145793(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LANCL1
• Ensembl ID: ENSECAG00000009197
• Aliases: None
• Description: LanC lantibiotic synthetase component C-like 1 (bacterial) [Source:HGNC Symbol;Acc:6508]

Sequence

>retro_ecab_944
GGACCGATGGGCCACATCCATGCTCTTCTCTTTGCCAATAAGCACTTTGGAGTGGAAAAGATTCCTCAAAGCCACATTCA
GTAGATTTGTGAAACAGTCTTAACCTCTGGAGAAAACCTAGCTAGAAAGAAGAATTTAACAGCAAAGACTCCACTGGTGT
ATGAATGGTACCAAGAATATTACGTGGGGGCTGCTCACGGCCTGGCAGGAATTTACTACCTCCTGATGCAGCCCAGCCTT
CAGGTGAGCCATGCGAAGTTACATAGTTTGGTCAAGCCCAGTGTAGACTATGTCTGCCAGCTGAAATTCCCTTCTGGCCA
TTGCCCTCCACGTGTGGACAATACTCAAGATCTGCTAGTCCACTGGTGCCACGGTGCCCCTGGGGTAATCTACATGCTCA
TCCAGGCCTATAAGGTGTTCAGAGAGGAGCGCTATCTCAGCGACGCCCGGCAGAGCGCTGACCTGACCTGGCAGTACGGG
CTGCTGAAGAAGGGCTACTGGCTGTGCCACGGCGCTGCGGGCAACGCCGACGCCTTCCTGGCGCTGTTCAACCTCACACA
GGCCAGGAAGTACCTGTACAGGGCCTGCAAGTTCGCTGAGTGATGCTTGGATTACGGAGAACATGGGTGCAGAACACCGG
ACAACCCCTTCTCCCTCTTTGAAGGAATGGCTGGAACAATCTATTTCCTGGCTGACCTGCTAGTGCCAGAGAAAGCCTGG
TTCCCTGCATTTGAACTG

Alignment

ORF - retro_ecab_944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.65 %
• Parental protein coverage: 61.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRMGYIYALLFVNKHFGVEKIPQSHIQQICETVLTSGENLARKRNFTAKTPLMYEWYQEYYVGAAHGLAG
          G.MG.I.ALLF.NKHFGVEKIPQSHIQ.ICETVLTSGENLARK.N.TAKTPL.YEWYQEYYVGAAHGLAG
Retrocopy GPMGHIHALLFANKHFGVEKIPQSHIQ*ICETVLTSGENLARKKNLTAKTPLVYEWYQEYYVGAAHGLAG

Parental  IYYFLMQPSLQVSHAKLHSLVKPSVDYVCQLKFPSGNYPPCVDDTRDLLVHWCHGAPGVIYMLIQAWKVF
          IYY.LMQPSLQVSHAKLHSLVKPSVDYVCQLKFPSG..PP.VD.T.DLLVHWCHGAPGVIYMLIQA.KVF
Retrocopy IYYLLMQPSLQVSHAKLHSLVKPSVDYVCQLKFPSGHCPPRVDNTQDLLVHWCHGAPGVIYMLIQAYKVF

Parental  REERYLTDARQSADLIWQYGLLKKGYGLCHGAAGNAYAFLALFNLTQDRKYLYRACKFAEWCLDYGEHGC
          REERYL.DARQSADL.WQYGLLKKGY.LCHGAAGNA.AFLALFNLTQ.RKYLYRACKFAE.CLDYGEHGC
Retrocopy REERYLSDARQSADLTWQYGLLKKGYWLCHGAAGNADAFLALFNLTQARKYLYRACKFAE*CLDYGEHGC

Parental  RTPDTPFSLFEGMAGTIYFLADLLVPEKARFPAFEL
          RTPD.PFSLFEGMAGTIYFLADLLVPEKA.FPAFEL
Retrocopy RTPDNPFSLFEGMAGTIYFLADLLVPEKAWFPAFEL

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	19.48 RPM
SRP021940_cerebellum	0.05 RPM	172.78 RPM
SRP021940_embryo	0.05 RPM	45.67 RPM
SRP021940_placental_villous	0.05 RPM	18.47 RPM
SRP021940_synovial_membrane	0.03 RPM	24.02 RPM
SRP021940_testis	5.82 RPM	299.77 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_944 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_944 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_944 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009197	1 retrocopy	retro_ecab_944 ,
Otolemur garnettii	ENSOGAG00000005620	1 retrocopy	retro_ogar_833,