RetrogeneDB ID: retro_fcat_1832

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:3866878..3867798(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000031910
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PEX13
• Ensembl ID: ENSFCAG00000028969
• Aliases: None
• Description: peroxisomal biogenesis factor 13 [Source:HGNC Symbol;Acc:8855]

Sequence

>retro_fcat_1832
ATGGCTTCCCAGCGCCGCCTCCCCCGAAACCCTGGGAGACCCGCCGAATTCCGGGGGCCGGGCCAGGACCAGGACCCGGC
CCCACTTTCCAATCTGCTGATTTGGGTTCTAGTTTATTGACAAGACCTGGACAACCAACACTTACCAGAGTGCCCCCACC
TATTCTTCCAAGGCCATCACAGCAGACAGGAAGCAGCACTGTGAATACTTTCAGACCTGCTTACAGTTCATTTTCTTCAG
GATATGGTGCCTATGGAAATTCGTTTTATGGAAGCTATAGCCCTTATAGTTATGGATATAATGGGTTGGGCTATAACCGC
CTCCGTGTAGATGATCTGCCACCCAGTAGATTTGTTCAGCAAGTTGAAGAAAGCAGCAGAGGTGCATTTCAGTCCATTGA
AAGTATTGTGCATGCATTTGCCTCTGTCAGTATGATGATGGATGCTACCTTTTCAGCTGTCTATAACAGTTTCAGGGCTG
TATTGGATGTAGCAAATCACTTTTCCCGATTAAAAATACATTTCACAAAGGTTTTTTCAGCTTTTGCATTAGTTAGGACT
ATAAGGTATCTTTACAGATGGTTACAGTGGATGATAGGTTTAAGAAGAGGCTCTGAGAATGAGGACCTATGGGCAGAAAG
TGAAGGAACTGTGGCTTGCCTTGGTGCCGAGGACAAAGCAGCTAATTCAGCCAAATCTTGGCCAATATTCTTGTTCTTTG
CTGTTATCCTTGGTGGTCCTTACTTCATCTGGAAACTTCTGTCTACCCATAATGATGAAGTCACAGACAACACCAACTGG
GCAAGTGGTGAGGATGACCATGTAGTTGCTAGAGCAGAATATGATTTTGCTGCTGTGTCCGAAGAAGAAATTTCTTTCCG
TGCTGGTGATATGCTAAACTTAGCTCTCAAAGCAACCCAA

Alignment

ORF - retro_fcat_1832 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.4 %
• Parental protein coverage: 76.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASQ-PPPPPKPWETRRIPGAGPGPGPGPTFQSADLGPSLLTRPGQPTLTRVPPPILPRPSQQTGSSNVN
          MASQ..PPPPKPWETRRIPGAGPGPGPGPTFQSADLG.SLLTRPGQPTLTRVPPPILPRPSQQTGSS.VN
Retrocopy MASQ<APPPPKPWETRRIPGAGPGPGPGPTFQSADLGSSLLTRPGQPTLTRVPPPILPRPSQQTGSSTVN

Parental  TFRPAYSSFSSGYGAYGNSFYGSYSPYSYGYNGLGYNRLRVDDLPPSRFVQQVEESSRGAFQSIESIVHA
          TFRPAYSSFSSGYGAYGNSFYGSYSPYSYGYNGLGYNRLRVDDLPPSRFVQQVEESSRGAFQSIESIVHA
Retrocopy TFRPAYSSFSSGYGAYGNSFYGSYSPYSYGYNGLGYNRLRVDDLPPSRFVQQVEESSRGAFQSIESIVHA

Parental  FASVSMMMDATFSAVYNSFRAVLDVANHFSRLKIHFTKVFSAFALVRTIRYLYRRLQWMIGLRRGSENED
          FASVSMMMDATFSAVYNSFRAVLDVANHFSRLKIHFTKVFSAFALVRTIRYLYR.LQWMIGLRRGSENED
Retrocopy FASVSMMMDATFSAVYNSFRAVLDVANHFSRLKIHFTKVFSAFALVRTIRYLYRWLQWMIGLRRGSENED

Parental  LWAESEGTVACLGAEDKAANSAKSWPIFLFFAVILGGPYLIWKLLSTHNDEVTDNTNWASGEDDHVVARA
          LWAESEGTVACLGAEDKAANSAKSWPIFLFFAVILGGPY.IWKLLSTHNDEVTDNTNWASGEDDHVVARA
Retrocopy LWAESEGTVACLGAEDKAANSAKSWPIFLFFAVILGGPYFIWKLLSTHNDEVTDNTNWASGEDDHVVARA

Parental  EYDFAAVSEEEISFRAGDMLNLALKEQQ
          EYDFAAVSEEEISFRAGDMLNLALK..Q
Retrocopy EYDFAAVSEEEISFRAGDMLNLALKATQ

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
SRP017611_brain	0.23 RPM	8.15 RPM
SRP017611_kidney	0.31 RPM	9.17 RPM
SRP017611_liver	0.81 RPM	14.05 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1832 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1832 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,