RetrogeneDB ID: retro_fcat_1789

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F1:51351370..51352237(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000028088
• Aliases: None
• Description: None

Sequence

>retro_fcat_1789
ATGAGCAGCAAAGAAGGATCAGGAGGTTCAGGAAAGGGAAGCATAACAGTTCCCCACATAACCAGAGAAGAGAAGGGAAG
GATGTTCATTCACCTGCACCTATGATATTGGCCTTCAAATCATTTCAGCAGAAACTTGATGCAAAACATGACAAATAGGA
GAGACTTGTGAAACTTTATGGAGATATAACTGTTAAACATAGAAGGACAATTTTTCATCTCCATTGGCTTACAAGTTCTC
CTGATATGGAAGAAATATTGACTGACTCGGAAATTAAATTGGATGGTATTAGACAAAAGGTGTTACAAGTAGCTCAAGAG
CTCTCCGGAGAAGACATGCATCAATTCCATAGAGCCGTTACTATAGGACTGAGGGAATATGTGGACATTATCTCTTTTCA
GCACCTCATTAGAACATGATCACTTACCAATATGGATGAAATTAAATAATTGATATTTACCACAGAATAATATGGAAAAG
AAAATGAGACCCCCTCCTTTGATGCACAGGATAAGGAGTTTGGGACTTGGAAACTAAAAATCACCCCTGTTGATTACCTT
CTGGGAGTGGCTCATTTAACTGGAGAGTTGATGCAGATGTGTATTAACAGATGGGGAAAGGGGGACATTGACACCCCCTT
TTGAGGTGAGCCAGTTTTTACATCAGGTTTATGATGGGTTTTTATTCACTGGCAATATGGACCTTATGCAGTTTCTAAGA
AGCTGTATACCTTGAGACAAAGTTTGGCCAAAGTGGATAATACTTGGTTATGCCTTTAAAGTCAGAGGTTCAGAAATTCC
AGAACATATGCTGGCAGATGTCTTTTCAGTTAAAACAGAAATGATTGATTAAGATAATGGCATTTCT

Alignment

ORF - retro_fcat_1789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSSKEGSGG-FRKRKHDNFPHNQRREGKDVNSSSPVMLAFKSFQQELDARHDKYERLVKLSRDITVESKR
          MSSKEGSGG.FRK.KH...PHNQRREGKDV.S..P..LAFKSFQQ.LDA.HDK.ERLVKL..DITV...R
Retrocopy MSSKEGSGG<FRKGKHNSSPHNQRREGKDVHSPAPMILAFKSFQQKLDAKHDK*ERLVKLYGDITVKHRR

Parental  TIFLLHRITSAPDMEEILTESEVKLDGVRQKILQVAQELSGEDMHQFHRAITTGLQEYVEAVSFQHFIKT
          TIF.LH..TS.PDMEEILT.SE.KLDG.RQK.LQVAQELSGEDMHQFHRA.T.GL.EYV...SFQH.I.T
Retrocopy TIFHLHWLTSSPDMEEILTDSEIKLDGIRQKVLQVAQELSGEDMHQFHRAVTIGLREYVDIISFQHLIRT

Parental  RSLISMDEINKQLIFTTEEYGKENKTPSSDAQDKQFGTWRLKITPVDYLLGVADLTGELMRMCINSVGNG
          .SL..MDEI.K.LIFTTE.YGKEN.TPS.DAQDK.FGTW.LKITPVDYLLGVA.LTGELM.MCIN..G.G
Retrocopy *SLTNMDEI-K*LIFTTE*YGKENETPSFDAQDKEFGTWKLKITPVDYLLGVAHLTGELMQMCINRWGKG

Parental  DIDT-PFEVSQFLRQVYDGFSFIGNT-GPYEVSKKLYTLKQSLAKVENAC-YALRVRGSEIPKHMLADVF
          DIDT.PFEVSQFL.QVYDGF.F.GN..GPY.VSKKLYTL.QSLAKV.N...YA..VRGSEIP.HMLADVF
Retrocopy DIDT>PFEVSQFLHQVYDGFLFTGNM<GPYAVSKKLYTLRQSLAKVDNTW>YAFKVRGSEIPEHMLADVF

Parental  SVKTEMIDQEEGIS
          SVKTEMID...GIS
Retrocopy SVKTEMID*DNGIS

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	31.10 RPM
SRP017611_kidney	0.00 RPM	30.81 RPM
SRP017611_liver	0.00 RPM	19.51 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1789 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1789 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002637	1 retrocopy	retro_amel_1655,
Dasypus novemcinctus	ENSDNOG00000006963	1 retrocopy	retro_dnov_1829,
Felis catus	ENSFCAG00000028088	1 retrocopy	retro_fcat_1789 ,
Myotis lucifugus	ENSMLUG00000015591	1 retrocopy	retro_mluc_1131,
Mus musculus	ENSMUSG00000056820	1 retrocopy	retro_mmus_393,
Otolemur garnettii	ENSOGAG00000005575	1 retrocopy	retro_ogar_91,
Ictidomys tridecemlineatus	ENSSTOG00000024989	1 retrocopy	retro_itri_259,