RetrogeneDB ID: retro_fcat_195

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:181946712..181947458(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000022849
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: THUMPD1
• Ensembl ID: ENSFCAG00000015158
• Aliases: None
• Description: THUMP domain containing 1 [Source:HGNC Symbol;Acc:23807]

Sequence

>retro_fcat_195
ATGGCGGCCCCCGTCCAGCAGCCTCCTCGGTCTAGCGGTGGAAAGCGCAAAGGGAAAGCTCAGTGTGTGCAGGCCAAGGG
GGCGCGGCGCTGCGACGGCGGTGGGCCACCGCAGCTGGAACCCGGGCTACAGGGCCTACTCATTACCTGCAACATGAACC
AGCGCAAGTGCGTGGAGGAGGCCTACAGTCTGCTCAACGAATACGGCTACGACGTGTACGGGCCGGAAAAGTTTACAAAG
ATCAGCAGCCCTCTGGAAGTGAGGCAGAAGATGATGATGTGGAGGCTGCCTTGAAGAAAGAAGTTGGTGGCATTAAAGCA
TCTACGGAGATGAAGCTAAGAAGATTCCAATCAGTGGAGAGTGGAGCAAATAACGTAGTCTTCATCAGGACACTTGGGAT
AGAACCTGAGAAATTGGTACGTCATATTCTTCAGGATATGTATAAAACCAAGAAGAAGAAGACTCGGGTTATTCTACGAA
TGTTACCTATTTCGGGCACATGCAAGGCTTTCTTAGAAGACATGAAAAAATATGCAGAAACATTTTTGGAACCCTGGTTT
AAAGCTCCAAATAAAGGGACATTTCAGATTGTATATAAATCTCGAAATAACATCCACATGAATAGAGAAGAAGTTATCAA
AGAATTGGCAGGAATAGTAGGCAGCCTCAATTCGGAAAATAAAGTGGATCTTACCAATCCACAGTACACAATGGTAGTGA
AAATCATTAAAGCTGTCTGTTGCCTG

Alignment

ORF - retro_fcat_195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.63 %
• Parental protein coverage: 76.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPVQQPPQSSGGKRKGKAQYVQAKRARRCDGGGPRQLEPGLQGILITCNMNERKCVEEAYSLLNEYGD
          MAAPVQQPP.SSGGKRKGKAQ.VQAK.ARRCDGGGP.QLEPGLQG.LITCNMN.RKCVEEAYSLLNEYG.
Retrocopy MAAPVQQPPRSSGGKRKGKAQCVQAKGARRCDGGGPPQLEPGLQGLLITCNMNQRKCVEEAYSLLNEYGY

Parental  DMYGPEKFTDKDQQP-SGSEGEDDDMEAALKKEVGDIKASTEMKLRRFQSVESGANNVVFIRTLGIEPEK
          D.YGPEKFT.K...P.SGSE.EDDD.EAALKKEVG.IKASTEMKLRRFQSVESGANNVVFIRTLGIEPEK
Retrocopy DVYGPEKFT-KISSP<SGSEAEDDDVEAALKKEVGGIKASTEMKLRRFQSVESGANNVVFIRTLGIEPEK

Parental  LVHHILQDMYKTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFLAPWFKAPNKGTFQIVYKSRNNSHMN
          LV.HILQDMYKTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFL.PWFKAPNKGTFQIVYKSRNN.HMN
Retrocopy LVRHILQDMYKTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFLEPWFKAPNKGTFQIVYKSRNNIHMN

Parental  REEVIKELAGIVGSLNSENKVDLTNPQYTVVVEIIKAVCCL
          REEVIKELAGIVGSLNSENKVDLTNPQYT.VV.IIKAVCCL
Retrocopy REEVIKELAGIVGSLNSENKVDLTNPQYTMVVKIIKAVCCL

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	0.00 RPM	9.07 RPM
SRP017611_kidney	0.00 RPM	4.53 RPM
SRP017611_liver	0.00 RPM	3.13 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_195 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_195 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009499	1 retrocopy	retro_cjac_915,
Cavia porcellus	ENSCPOG00000008919	1 retrocopy	retro_cpor_71,
Felis catus	ENSFCAG00000015158	1 retrocopy	retro_fcat_195 ,
Homo sapiens	ENSG00000066654	1 retrocopy	retro_hsap_2521,
Gorilla gorilla	ENSGGOG00000005231	1 retrocopy	retro_ggor_1573,
Macaca mulatta	ENSMMUG00000004225	1 retrocopy	retro_mmul_1599,
Monodelphis domestica	ENSMODG00000006971	1 retrocopy	retro_mdom_54,
Nomascus leucogenys	ENSNLEG00000012369	1 retrocopy	retro_nleu_1443,
Pan troglodytes	ENSPTRG00000007848	1 retrocopy	retro_ptro_1466,