RetrogeneDB ID: retro_ecab_247

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:902588..903020(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLS1
• Ensembl ID: ENSECAG00000023869
• Aliases: None
• Description: cardiolipin synthase 1 [Source:HGNC Symbol;Acc:16148]

Sequence

>retro_ecab_247
GCCAATCAAAAATCAGCTTTGGGACATGCTCTAACCACTTGTTGATAAAAATACTTATCGGTATCTTATATGTTCACTTG
TCCTATGCAGACCTTACTCCAGTTCCACTGACTGGTATGATAATTTCAAGAGATGCAGTGTTGACTGCTGCTGTTTTTTA
TGTCAGATATCAGACTCTTCCAACACCACAAACACTTTCTAAGCGTTCCAGTCCTCGCTCTGCCACTGCTAGGTTAAAAC
TAACTTTCATCAGCAAAGGAAATAAAAAGGTCCAGCTATCTTGGTGACAGCTTCTTGGCAGCTCCAGTTTTCGATTGTGC
TGACAGCATCTATCTTCAGATACAGTGGATTTTTATAGTTTTCACCACAGTTGCATCAGCTTACAGTTATTATCATTATG
GTCAGAAAACTGTTCAGGTGATAAAAGGCAGA

Alignment

ORF - retro_ecab_247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.65 %
• Parental protein coverage: 72.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASQKSALGSAL-DPLADKILISVLYVSLTYADLIPVPLTYMIISRDVMLIAAVFYVRYRTLPTPRTLSKY
          A.QKSALG.AL...L..KILI..LYV.L.YADL.PVPLT.MIISRD..L.AAVFYVRY.TLPTP.TLSK.
Retrocopy ANQKSALGHAL<NHLLIKILIGILYVHLSYADLTPVPLTGMIISRDAVLTAAVFYVRYQTLPTPQTLSKR

Parental  FNPCYATARLKPTFISKVNTAVQL-ILVAAS-LAAPVFNYADSIYLQILWCFTAFTTAASAYSYYHYGRK
          ..P..ATARLK.TFISK.N..VQL.ILV.AS.LAAPVF..ADSIYLQI.W.F..FTT.ASAYSYYHYG.K
Retrocopy SSPRSATARLKLTFISKGNKKVQL<ILVTAS<LAAPVFDCADSIYLQIQWIFIVFTTVASAYSYYHYGQK

Parental  TVQVIKGK
          TVQVIKG.
Retrocopy TVQVIKGR

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	4.78 RPM
SRP021940_cerebellum	0.00 RPM	6.34 RPM
SRP021940_embryo	0.00 RPM	8.54 RPM
SRP021940_placental_villous	0.00 RPM	7.31 RPM
SRP021940_synovial_membrane	0.00 RPM	6.09 RPM
SRP021940_testis	0.00 RPM	23.21 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_247 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_247 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_247 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010596	1 retrocopy	retro_amel_1758,
Bos taurus	ENSBTAG00000000065	1 retrocopy	retro_btau_1167,
Canis familiaris	ENSCAFG00000005934	1 retrocopy	retro_cfam_1002,
Equus caballus	ENSECAG00000023869	2 retrocopies	retro_ecab_247 , retro_ecab_930,
Felis catus	ENSFCAG00000023647	1 retrocopy	retro_fcat_1393,
Microcebus murinus	ENSMICG00000011666	1 retrocopy	retro_mmur_751,
Mustela putorius furo	ENSMPUG00000006349	1 retrocopy	retro_mputfur_1021,
Rattus norvegicus	ENSRNOG00000021273	3 retrocopies	retro_rnor_2865, retro_rnor_2866, retro_rnor_2977,