RetrogeneDB ID: retro_fcat_213

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:156859..157503(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHB2
• Ensembl ID: ENSFCAG00000027063
• Aliases: None
• Description: pleckstrin homology domain containing, family B (evectins) member 2 [Source:HGNC Symbol;Acc:19236]

Sequence

>retro_fcat_213
ATGGTGTTTGTAAAGAGCGGATGGTTGCTGCGACAGAGTACCATTTTGAAGCATTGGGAGAAGAATTGGTTTGACCTGTG
GTCAGATGTTACCTGATCTATTATGATAACTAAACTTGGCAAAGTGTTGAAGACAAGGTCCACATGCCAGTGGACTTTAT
CAACATCTGCATGGGGCATGAGTGTCAGGATACTCAGCCTCCAGATGGGAAACCAAAAGACTGTACGCTGAAGATTGTTT
GCTGAGATGGGAAAACCATGCATCTTTGTGCAGAAAGCACAGAGGATTGTTTGGCCTGGAAATTTACACTCCAGGATTCC
AGGACAAACACAGCTTATGTTGGCTCAGAAATCCTGTATGATAAGACAGCCGTGACTTCTTCCTCTCCTCCTCACACAGC
CTATGGGACACCAACCTCTGAGGCATATGGCTATGGTCCATACAGTGGTGCATAGCCTCCAGGAACTCAAGCTATCTATT
GTTCTGTATCCTGCCAGTACCCACATGAAGGACTTTATGGACAACAGCCTGCCAACCAAGTCATCATTCGGGAGTGGTAT
CGAGACAGTGACAGTGATCTGGCACTGGACATGGTGGCCAGAGCTGCCACAGGCATGGCCTTAGGCTCTCTGGTCTGGGT
CTTC

Alignment

ORF - retro_fcat_213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAFVKSGWLLRQSTILKRWKKNWFDLWSDG-HLIYYDDQTRQSVEDKVHMPVDCINIRMGHECRDIQPPD
          M.FVKSGWLLRQSTILK.W.KNWFDLWSD...LIYYD..T.QSVEDKVHMPVD.INI.MGHEC.D.QPPD
Retrocopy MVFVKSGWLLRQSTILKHWEKNWFDLWSDV<YLIYYDN*TWQSVEDKVHMPVDFINICMGHECQDTQPPD

Parental  GKSKDCMLQIVCRDGKTISLCAESTDDCLAWKFTLQDSRTNTAYVGSEVLYDETAVASSPPPYTAYAAPT
          GK.KDC.L.IVC.DGKT..LCAEST.DCLAWKFTLQDSRTNTAYVGSE.LYD.TAV.SS.PP.TAY..PT
Retrocopy GKPKDCTLKIVC*DGKTMHLCAESTEDCLAWKFTLQDSRTNTAYVGSEILYDKTAVTSSSPPHTAYGTPT

Parental  PEQAYGYGPYSGAYPPGTQVVYAASGQAYAVPYQYPYAGLYGQQPANQIIIRERYRDSDSDLALGMLAGA
          .E.AYGYGPYSGA.PPGTQ..Y......Y..P....Y......Q.......R....D...D.......G.
Retrocopy SE-AYGYGPYSGA*PPGTQAIYCSVSCQY--PHEGLYGQQPANQVIIREWYRDSDSDLALDMVARAATGM

Parental  ATGMALGSLFWVF
          A.G....SL.WVF
Retrocopy ALG----SLVWVF

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	36.96 RPM
SRP017611_kidney	0.10 RPM	21.54 RPM
SRP017611_liver	0.00 RPM	5.46 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_213 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_213 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000941	2 retrocopies	retro_btau_1134, retro_btau_1635,
Cavia porcellus	ENSCPOG00000026329	1 retrocopy	retro_cpor_985,
Equus caballus	ENSECAG00000017331	1 retrocopy	retro_ecab_1069,
Felis catus	ENSFCAG00000027063	1 retrocopy	retro_fcat_213 ,
Homo sapiens	ENSG00000115762	1 retrocopy	retro_hsap_1890,
Meleagris gallopavo	ENSMGAG00000001052	1 retrocopy	retro_mgal_17,
Monodelphis domestica	ENSMODG00000018634	1 retrocopy	retro_mdom_720,
Nomascus leucogenys	ENSNLEG00000010698	2 retrocopies	retro_nleu_1471, retro_nleu_2016,
Oryctolagus cuniculus	ENSOCUG00000024282	1 retrocopy	retro_ocun_654,
Otolemur garnettii	ENSOGAG00000028408	2 retrocopies	retro_ogar_2771, retro_ogar_703,
Pongo abelii	ENSPPYG00000012740	1 retrocopy	retro_pabe_1570,
Ictidomys tridecemlineatus	ENSSTOG00000020509	1 retrocopy	retro_itri_56,