RetrogeneDB ID: retro_ecab_249

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:3802215..3802824(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPCDC
• Ensembl ID: ENSECAG00000019339
• Aliases: None
• Description: phosphopantothenoylcysteine decarboxylase [Source:HGNC Symbol;Acc:28107]

Sequence

>retro_ecab_249
ATGGAAGCAAGGGCCTCGTGTCCAGCTGCTGCCCCCTCGGTGGAGGGACAGTTCCGTGTTCTCGTGGGTGTCACTGGGAG
TGTTGCAGCTCTGAAGTTGCCCCTTCTGGTGCGAAGGCTTTTGGATATTCCTGGCCTGGAAGTAGCAGTAGTTAAAACTG
AGAGAGCCAAACATTTCTACACTCCCAGGATGTTCCTGTCACCCTCGACAGCAATGCTGATGGATGGGAGATGTGGCAGC
GCCGATCTGATCCACTTCTCCACATTGACCTGCGGCAGTGCGCAGACCTGATGCTGGTGGCTCCTCTTGATGCCAATACT
CTGGGGAAGGTGGCTAGAGGCATCTGTGACAACTTGCTTACCTGTGTCATCCGGGCCTGGGACTGCAGCAAGCCTCTGCT
CTTCTGCCCGGCGATGAACACTGCCTGTGGGAGCACCCCATCACCGCGCAGCAGGGGGGCCAGCTCAAGGCCTTCGCTAC
GTCGAGATTCCCTGTGTGGCCAAGAAGCTGGTGTGTGGAGACCAACATCTGGGGGCCATGGCTGCAGTGGGCACCATTGT
GGACAGAGTGAAAGAGATCCTCCCCCTTCACAGTGGCTTCCAGCAGAGT

Alignment

ORF - retro_ecab_249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEARASCPAAAPLVERQFHVLVGVTGSVAALKLPLLVSRLLDIPGLEVAVVTTERAKHFYTP-QDVPVTL
          MEARASCPAAAP.VE.QF.VLVGVTGSVAALKLPLLV.RLLDIPGLEVAVV.TERAKHFYTP.QDVPVTL
Retrocopy MEARASCPAAAPSVEGQFRVLVGVTGSVAALKLPLLVRRLLDIPGLEVAVVKTERAKHFYTP<QDVPVTL

Parental  YSDADEWEMWKRRSDPVLHIDLRKWADLMLVAPLDANTLGKVASGICDNLLTCVIRAWDRSKPLLFCPAM
          .S.AD.WEMW.RRSDP.LHIDLR..ADLMLVAPLDANTLGKVA.GICDNLLTCVIRAWD.SKPLLFCPAM
Retrocopy DSNADGWEMWQRRSDPLLHIDLRQCADLMLVAPLDANTLGKVARGICDNLLTCVIRAWDCSKPLLFCPAM

Parental  NTA-MWEHPITAQQVGQLKAFG-YVEIPCVAKKLVCGDQGLGAMAEVGTIVDKVKEILSLHGGFQQS
          NTA..WEHPITAQQ.GQLKAF..YVEIPCVAKKLVCGDQ.LGAMA.VGTIVD.VKEIL.LH.GFQQS
Retrocopy NTA<LWEHPITAQQGGQLKAFA<YVEIPCVAKKLVCGDQHLGAMAAVGTIVDRVKEILPLHSGFQQS

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	0.59 RPM
SRP021940_cerebellum	0.00 RPM	2.44 RPM
SRP021940_embryo	0.00 RPM	1.53 RPM
SRP021940_placental_villous	0.05 RPM	1.64 RPM
SRP021940_synovial_membrane	0.00 RPM	1.51 RPM
SRP021940_testis	0.00 RPM	11.19 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_249 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_249 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	ENSECAG00000019339	1 retrocopy	retro_ecab_249 ,