RetrogeneDB ID: retro_fcat_1101

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:83056157..83056590(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED21
• Ensembl ID: ENSFCAG00000030691
• Aliases: None
• Description: mediator complex subunit 21 [Source:HGNC Symbol;Acc:11473]

Sequence

>retro_fcat_1101
ATGGCTGATAGGCTCACACAGCTGCAGGACGTGGTGAGTGCCCTTGCAGATCAGTTTTGTAATGCCATTGGAGTGTTACA
GCATTGTGGCCCTCCCGCCCCTTTTCCTGATGCTCAGACAGCAATGAATGAAGATCTGCCAACTAATCCTACAGAAGAAT
ACGTCTAGCTTTTTGCCGCACTGATCCCAAGAACAGCAAAAGACATGGATGTTTTGGTCCATTCATTACTCAGTGAAAAA
TCTACAGCTGCTTTACATACAGGCTGCTAGCTTGTACAAGCTGGAAGAAGAAAGCCACGAAGCTGCTACATATCTGGAGG
ATGTTATTTATAGAGGGGATGGGCTTCTGGAATAGATACAAAGCACACTTGCTCCTGTTGCATAGTCACAACTGGAGACG
AGGAGTAGTACCCATCCCCAGTCTCTCCCAGAC

Alignment

ORF - retro_fcat_1101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.41 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANPTEEYAQLFAALIARTAKDID
          MADRLTQLQD.V..LADQFCNAIGVLQ.CGPPA.F...QTA.N.D.P.NPTEEY..LFAALI.RTAKD.D
Retrocopy MADRLTQLQDVVSALADQFCNAIGVLQHCGPPAPFPDAQTAMNEDLPTNPTEEYV*LFAALIPRTAKDMD

Parental  VLIDS-LPSEESTAA-LQAASLYKLEEENHEAATCLEDVVYRGDMLLEKIQSALADIAQSQLKTRSGTHS
          VL..S.L......A...QAASLYKLEEE.HEAAT.LEDV.YRGD.LLE.IQS.LA..A.SQL.TRS.TH.
Retrocopy VLVHSLLSEKSTAAL>IQAASLYKLEEESHEAATYLEDVIYRGDGLLE*IQSTLAPVA*SQLETRSSTHP

Parental  QSLPD
          QSLPD
Retrocopy QSLPD

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	24.45 RPM
SRP017611_kidney	0.00 RPM	26.69 RPM
SRP017611_liver	0.00 RPM	7.18 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1101 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1101 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011670	1 retrocopy	retro_amel_108,
Dasypus novemcinctus	ENSDNOG00000010041	1 retrocopy	retro_dnov_998,
Echinops telfairi	ENSETEG00000006223	1 retrocopy	retro_etel_1141,
Felis catus	ENSFCAG00000030691	1 retrocopy	retro_fcat_1101 ,
Homo sapiens	ENSG00000152944	1 retrocopy	retro_hsap_4105,
Gorilla gorilla	ENSGGOG00000016313	1 retrocopy	retro_ggor_2756,
Myotis lucifugus	ENSMLUG00000007678	1 retrocopy	retro_mluc_229,
Nomascus leucogenys	ENSNLEG00000005431	1 retrocopy	retro_nleu_573,
Pongo abelii	ENSPPYG00000004377	1 retrocopy	retro_pabe_3361,
Ictidomys tridecemlineatus	ENSSTOG00000008391	2 retrocopies	retro_itri_1005, retro_itri_1057,