RetrogeneDB ID: retro_fcat_977

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:85099110..85099583(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX7
• Ensembl ID: ENSFCAG00000002292
• Aliases: None
• Description: syntaxin 7 [Source:HGNC Symbol;Acc:11442]

Sequence

>retro_fcat_977
CCAGAAGATCACACAATGTTGCAACAGAAGCAGCAGTATACTACCCAACTTGCCAAAGAGACCGGTAAGTACATTAAAGA
GTTTGGATCCCTGCCCACCACCCCCAGCGAACAGCATCAAAGGAAAATGCAGAAAGATCCCTTAATGGCTCAATTCACTA
CATCACTGACAAACTTTCAAAAGGTCCAGAGGGAAGCTGCTGAGAAAGAGAAAGAGTTTGTTGCTCAAGTAAGAGCCAGT
TCTAGAGTATCTGGTGGTTTTCCTGAGGACAGCTCAAAGGACAGGAATCTTGTATCCTGGGAAAGCAAGCTCAACCTCAG
GTGCAGGTGCAGAATGAAAATATTACAGATGATGACCTCTGCCTTATTCATGAGAGAGAATCTTCTATTAGGCAACTTGA
AGCTGATATTATGGATATTAATGAAATATTTAAAGATTTGGGAATGATGATTCACGAGCAAGGAGATGTAATA

Alignment

ORF - retro_fcat_977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 60.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PELRQQLQQKQQYTNQLAKETDKYIKEFGSLPTTPSEQRQRKIQKDRLVAQFTTSLTNFQKVQREAAEKE
          PE....LQQKQQYT.QLAKET.KYIKEFGSLPTTPSEQ.QRK.QKD.L.AQFTTSLTNFQKVQREAAEKE
Retrocopy PEDHTMLQQKQQYTTQLAKETGKYIKEFGSLPTTPSEQHQRKMQKDPLMAQFTTSLTNFQKVQREAAEKE

Parental  KEFVARVRASSRVSGGFPEDTSKERNLVSWES-QAQPQVQVQDEEITEDDLRLIHERESSIRQLEADIMD
          KEFVA.VRASSRVSGGFPED.SK.RNLVSWES.QAQPQVQVQ.E.IT.DDL.LIHERESSIRQLEADIMD
Retrocopy KEFVAQVRASSRVSGGFPEDSSKDRNLVSWES<QAQPQVQVQNENITDDDLCLIHERESSIRQLEADIMD

Parental  INEIFKDLGMMIHEQGDVI
          INEIFKDLGMMIHEQGDVI
Retrocopy INEIFKDLGMMIHEQGDVI

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	0.23 RPM	40.86 RPM
SRP017611_kidney	0.10 RPM	32.98 RPM
SRP017611_liver	0.10 RPM	16.28 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_977 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_977 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010117	3 retrocopies	retro_chof_1503, retro_chof_2631, retro_chof_829,
Dasypus novemcinctus	ENSDNOG00000000295	1 retrocopy	retro_dnov_600,
Felis catus	ENSFCAG00000002292	1 retrocopy	retro_fcat_977 ,
Felis catus	ENSFCAG00000029657	1 retrocopy	retro_fcat_1701,
Myotis lucifugus	ENSMLUG00000004301	1 retrocopy	retro_mluc_494,
Sarcophilus harrisii	ENSSHAG00000014440	1 retrocopy	retro_shar_430,
Tursiops truncatus	ENSTTRG00000009853	1 retrocopy	retro_ttru_185,