RetrogeneDB ID: retro_ecab_122

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:34523005..34523492(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM41B
• Ensembl ID: ENSECAG00000026871
• Aliases: None
• Description: transmembrane protein 41B [Source:HGNC Symbol;Acc:28948]

Sequence

>retro_ecab_122
TTGCAAACATTTGCTATTCCGGGCTCTATATTTCTCAGTATACTCTTAGGGTTTCTTCAACCCTTTCCGCTAGCCTTATT
TCTTGTTTGTTTGTGTTCTGGACTTGGTGCCTCATTCTGCTATATGCTCTGCTATTTAGTTGTAAACAAATACGTAACAG
AGAAAGCAGTAAAATGGTCATAGCGGGTTGAACGTCATGGAGAACATGTCATTAACTACATTATATTTTTGAGAATAACA
CCATTTCTGCCTAATTGCTAATATTATGTCTCCTGTGATAAACGTGCCATTGAAATTTTTCTTATTGGCACTTTTCTAGG
TGTCACACCTCCCTCTTTTGTAGCGATTAAGGGCGTGAACAACACTGTACCAGCTCACAATCACAGAGGAAGCTATTTCC
TGCAACCCAGTATTTGTTCTAACAGTTTTGGCTCTTCTTTCTATTCTGCCAGCCATCTTCCAAAAAAAACTAAAGCAACA
ATTTGAG

Alignment

ORF - retro_ecab_122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.76 %
• Parental protein coverage: 57.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQTFAIPGSIFLSILSGFLYPFPLALFLVCLCSGLGASFCYMLSYLVGRPVVYKYLTEKAVKWSQQVERH
          LQTFAIPGSIFLSIL.GFL.PFPLALFLVCLCSGLGASFCYML.YLV....V.KY.TEKAVKWS..VERH
Retrocopy LQTFAIPGSIFLSILLGFLQPFPLALFLVCLCSGLGASFCYMLCYLV----VNKYVTEKAVKWS*RVERH

Parental  REHLINYIIFLRITPFLPN--WFINITSPVINVPLKVFFIGTFLGVAPPSFVAIK-AGTTLYQLTTAGEA
          .EH.INYIIFLRITPFLPN...........I...L...F.G....V.PPSFVAIK.A.TTLYQLT...EA
Retrocopy GEHVINYIIFLRITPFLPNC*YYVSCDKRAIEIFLIGTFLG----VTPPSFVAIK>A*TTLYQLTITEEA

Parental  VSWNSVFVLMILALLSILPAIFQKKLKQKFE
          .S.N.VFVL..LALLSILPAIF...LKQ.FE
Retrocopy ISCNPVFVLTVLALLSILPAIFXXXLKQQFE

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	3.95 RPM
SRP021940_cerebellum	0.00 RPM	7.53 RPM
SRP021940_embryo	0.00 RPM	5.45 RPM
SRP021940_placental_villous	0.00 RPM	11.02 RPM
SRP021940_synovial_membrane	0.00 RPM	4.83 RPM
SRP021940_testis	0.00 RPM	6.33 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_122 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_122 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
Equus caballus	ENSECAG00000026871	1 retrocopy	retro_ecab_122 ,
Loxodonta africana	ENSLAFG00000006953	1 retrocopy	retro_lafr_1229,
Mus musculus	ENSMUSG00000047554	1 retrocopy	retro_mmus_3296,