RetrogeneDB ID: retro_fcat_1634

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:57345999..57346205(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP1LC3A
• Ensembl ID: ENSFCAG00000022040
• Aliases: None
• Description: microtubule-associated protein 1 light chain 3 alpha [Source:HGNC Symbol;Acc:6838]

Sequence

>retro_fcat_1634
ATGCCTTCGGAGAAGATCTTCAAGCAGCACCACACCTTCCAACAAAGAACAGAAGATGTCCGACTTATCCGAGAGCCCCC
GCATCCTATGAAAATCCCAGTGATAATAGAACAGTACAAGGGTGAGAGCTACTTCCTGTCCTGGACAAAACCAAGTTTCT
TGTACCTGATCACATCAACATGAGTGAGCTCATCAAGATCTTTAGG

Alignment

ORF - retro_fcat_1634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.14 %
• Parental protein coverage: 54.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPSDRPFKQRRTFADRCKEVQQIRDQ-HPSKIPVIIERYKGEKQ-LPVLDKTKFLVPDHVNMSELVKIIR
          MPS...FKQ..TF..R...V..IR...HP.KIPVIIE.YKGE...LPVLDKTKFLVPDH.NMSEL.KI.R
Retrocopy MPSEKIFKQHHTFQQRTEDVRLIREPPHPMKIPVIIEQYKGESY<LPVLDKTKFLVPDHINMSELIKIFR

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	37.42 RPM
SRP017611_kidney	0.00 RPM	16.08 RPM
SRP017611_liver	0.00 RPM	4.25 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1634 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1634 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000012407	1 retrocopy	retro_etel_1766,
Felis catus	ENSFCAG00000001938	4 retrocopies	retro_fcat_1727, retro_fcat_1874, retro_fcat_340, retro_fcat_884,
Felis catus	ENSFCAG00000022040	1 retrocopy	retro_fcat_1634 ,
Monodelphis domestica	ENSMODG00000002694	1 retrocopy	retro_mdom_1256,
Mustela putorius furo	ENSMPUG00000017814	1 retrocopy	retro_mputfur_1049,
Ictidomys tridecemlineatus	ENSSTOG00000006158	2 retrocopies	retro_itri_287, retro_itri_988,