RetrogeneDB ID: retro_ecab_403

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:737192..738400(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000000155
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PEX13
• Ensembl ID: ENSECAG00000019622
• Aliases: None
• Description: peroxisomal biogenesis factor 13 [Source:HGNC Symbol;Acc:8855]

Sequence

>retro_ecab_403
ATGGCATCCCAGCCGCCACAGCCCCCGATACCCGGGGAGACCCACCGAATTCCGGGGGCTGGTCCGGGACCAGGACCCGG
CCCCACTTTCCAATCTGCTGATTTGGGTCCTACTTTATTGACAAGACCTGGACAACCAACACTTACCAGAGTGCCGCCAC
CTATTCTTCCAAGGCCATCACAGCAGACAGGAAGCAGCAGTGTGAACACTTTTAGACCTACTTACAGTTCATTTTCTTCT
GGATATGGTGCCTATGGAAATTCATTTTATGGAAGCTATAGCCCTTATAGTTATGGATATAATGGGTTGGGCTATAACCG
CATCCGTGTGGATGATCTTCCACCTAGTAGATTTGTTCAGCAAGCTGAAGAAAGCAGCAGAGGTGCATTTCACTCCATTG
AAAGTATTGTGCATGCATTTGCCTCTGTCAGTATGATGATGGATGCTACCTTTCCAGCTGTCTATAACAGTTTCAGGGCT
GTATTGCATGTAGCAAATCACTTTTCCCGATTAAAAATACACTTCACAAAGGTCTTTTCAGCTTTTGCATTAGTTGGGAC
TATAAGGTATCTTTATAGACGGTTACAGCAGATGATAGGTTTAAGAGGAGGCTCTGAGAATGAGGACTTATGGGCAGAAA
GTGAAGGAACTGTGGCTTGCCTTGGTGCCGAGGACAGAGCAGCTAATTCAGCAAAATCTTGGCCAATATTCTTATTCTTT
GCTGTTATCCTTGGTGGTCCTTATCTCATCTGGAAACTGCTGTCTATCCACACTGATGAAGTAACAGACAACACCAACTG
GGCAAGTGGTGAGGATGACCATGTAGTTGCTAGGGCAGAATATGATTTTACTGCTGCATCTGAAGAAGAAATTTCTTTCC
GTGCTGGTGATATGCTACATTTAGCTCTCAAAGAACAGCAACCCAAGTGCGTGGTTGGCTTCTGGCTAGTCTTGATGGTC
AAACAACAGGACTTATACCTGCTAATTATGTCAAAATTCTTGGTAAAAGAAGAGGTAGAAAAACAGTGGAATCCAGTAAA
ATTCCCAAGCAGCAACAATCTTTTACCAACACAACACTAATTAAAGGAGTCACGGCCACTGATTCTTTGGATGAACAGGA
AGCTGCCTTTGAATCTGTTTTTGTTGAAACTTGTAAGGTTCCAGTTGCACCTGATTCCACTGGGAAAAGTGGAGATAAAC
AAGTTCTT

Alignment

ORF - retro_ecab_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASQPPPPPKPWETRRIPGAGPGPGPGPTFQSADLGPTLLTRPGQPTLTRVPPPILPRPSQQTGSSSVNT
          MASQPP.PP.P.ET.RIPGAGPGPGPGPTFQSADLGPTLLTRPGQPTLTRVPPPILPRPSQQTGSSSVNT
Retrocopy MASQPPQPPIPGETHRIPGAGPGPGPGPTFQSADLGPTLLTRPGQPTLTRVPPPILPRPSQQTGSSSVNT

Parental  FRPAYSSFSSGYGAYGNSFYGSYSPYSYGYNGLGYNRLRLDDLPPSRFVQQAEESSRGAFQSIESIVHAF
          FRP.YSSFSSGYGAYGNSFYGSYSPYSYGYNGLGYNR.R.DDLPPSRFVQQAEESSRGAF.SIESIVHAF
Retrocopy FRPTYSSFSSGYGAYGNSFYGSYSPYSYGYNGLGYNRIRVDDLPPSRFVQQAEESSRGAFHSIESIVHAF

Parental  ASVSMMMDATFSAVYNSFRAVLDVANHFSRLKIHFTKVFSAFALVRTIRYLYRRLQRMIGLRGGSENEDL
          ASVSMMMDATF.AVYNSFRAVL.VANHFSRLKIHFTKVFSAFALV.TIRYLYRRLQ.MIGLRGGSENEDL
Retrocopy ASVSMMMDATFPAVYNSFRAVLHVANHFSRLKIHFTKVFSAFALVGTIRYLYRRLQQMIGLRGGSENEDL

Parental  WAESEGTVACLGAEDRAANSAKSWPIFLFFAVILGGPYLIWKLLSTHTDEVTDNTNWASGEDDHVVARAE
          WAESEGTVACLGAEDRAANSAKSWPIFLFFAVILGGPYLIWKLLS.HTDEVTDNTNWASGEDDHVVARAE
Retrocopy WAESEGTVACLGAEDRAANSAKSWPIFLFFAVILGGPYLIWKLLSIHTDEVTDNTNWASGEDDHVVARAE

Parental  YDFTAASEEEISFRAGDMLHLALKEQQPK-VRGWLLASLDGQTTGLIPANYVKILGKRRGRKTVESSKIP
          YDFTAASEEEISFRAGDMLHLALKEQQPK.VRGWLLASLDGQTTGLIPANYVKILGKRRGRKTVESSKIP
Retrocopy YDFTAASEEEISFRAGDMLHLALKEQQPK<VRGWLLASLDGQTTGLIPANYVKILGKRRGRKTVESSKIP

Parental  KQQQSFTNTTLIKGATAADSLDEQEAAFESVFVETCKVPVAPDSTGKSGDKQDL
          KQQQSFTNTTLIKG.TA.DSLDEQEAAFESVFVETCKVPVAPDSTGKSGDKQ.L
Retrocopy KQQQSFTNTTLIKGVTATDSLDEQEAAFESVFVETCKVPVAPDSTGKSGDKQVL

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	3.25 RPM
SRP021940_cerebellum	0.00 RPM	2.75 RPM
SRP021940_embryo	0.05 RPM	4.55 RPM
SRP021940_placental_villous	0.00 RPM	4.33 RPM
SRP021940_synovial_membrane	0.03 RPM	2.61 RPM
SRP021940_testis	0.13 RPM	12.34 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_403 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_403 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012871	1 retrocopy	retro_chof_282,
Equus caballus	ENSECAG00000019622	1 retrocopy	retro_ecab_403 ,
Felis catus	ENSFCAG00000028969	1 retrocopy	retro_fcat_1832,
Mus musculus	ENSMUSG00000020283	1 retrocopy	retro_mmus_1932,