RetrogeneDB ID: retro_fcat_1989

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:60099989..60100724(-)
• Located in intron of: ENSFCAG00000007121

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFPQ
• Ensembl ID: ENSFCAG00000031287
• Aliases: None
• Description: splicing factor proline/glutamine-rich [Source:HGNC Symbol;Acc:10774]

Sequence

>retro_fcat_1989
CAGCTTTGAGTTCACTTTGCCATACGTGCTGCCCTTTCCATTCAGAATTTTAATCTTATGTTTCCAATGAACTGTTGGAA
GAAGTCTTTTGCCAGTTTGGTCCTATTGAAAGGGCTGTTGTAATTGTGGATGATCACAGAAAACCTGCAGGGAAAGGCAT
TGTTGAATTTGCTTCTAAACCAGCAGCAAGAATAGCATGTGAAAGATGCAGTGAGAGTGTTTTTCTTACTGACAACTCCT
TGTCCAGTCATTGTGGAACCACCCAAACAATTAGATGATGAAGATGGTCTTCCTGAAGAACTCGCACAGAAGAATTCAGT
GTATTAAAATGAGACAGAAACCCCTACTCATTTTGCCTAGTATGGCACATTTGAGTATGAATATTTTCAGCAATGGAAGC
CCTTGAATAAAATGGAAAAACATCAAAGGAAACAAATCAATAAAAACATGAAAGATATGCAAGACAAATTGAAAAGTGAA
ATGGGAGATGCCTATCGTGAGCATCAAGCAAATATTTTGCATGAAGATCTGATGGGACACTAGGAGGAATTAAGACACAT
GGAAGAACTTCACAATCAAGAAATGAAGAAATATAAAGAAATGCAAGTAAGGCAACAGAGAATAATGTAGAAGGGAAAAG
AGATGAAGAGTGGTCAACGTGAGATGGAAGAATAAATGAGACATCAAAGAGAGTAAAGTTATAGCAGATGGGTAGAGGGA
TCCAAGAGAAAGAGA

Alignment

ORF - retro_fcat_1989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.2 %
• Parental protein coverage: 53.22 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QLRVRFATHAAALSVRNLS-PYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFE
          QL.V.FA..AA.LS..N....YVSNELLEE.F.QFGPIERAVVIVDD.....GKGIVEFASKPAAR.A.E
Retrocopy QL*VHFAIRAA-LSIQNFN<SYVSNELLEEVFCQFGPIERAVVIVDDHRKPAGKGIVEFASKPAARIACE

Parental  RCSEGV-FLLTTTPRPVIVEPLEQLDDEDGLPEKLAQKNPMYQKERETPPRFAQHGTFEYEYSQRWKSLD
          RCSE.V.FLLT.TP.PVIVEP..QLDDEDGLPE.LAQKN..Y..E.ETP..FA..GTFEYEY.Q.WK.L.
Retrocopy RCSESV>FLLT-TPCPVIVEPPKQLDDEDGLPEELAQKNSVY*NETETPTHFA*YGTFEYEYFQQWKPLN

Parental  EMEKQQREQVEKNMKDAKDKLESEMEDAYHEHQANLLRQDLMRRQEELRRMEELHNQEMQKRKEMQLRQE
          .MEK.QR.Q..KNMKD..DKL.SEM.DAY.EHQAN.L..DLM...EELR.MEELHNQEM.K.KEMQ.RQ.
Retrocopy KMEKHQRKQINKNMKDMQDKLKSEMGDAYREHQANILHEDLMGH*EELRHMEELHNQEMKKYKEMQVRQQ

Parental  EERRRREEEMMIRQREMEEQMRRQREESYSRMGYMDPRER
          ........EM...QREMEE.MR.QRE.SYSR......R.R
Retrocopy RIM*KGK-EMKSGQREMEE*MRHQRE*SYSRWVEGSKRKR

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	168.14 RPM
SRP017611_kidney	0.00 RPM	102.03 RPM
SRP017611_liver	0.00 RPM	75.72 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1989 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1989 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003595	1 retrocopy	retro_cfam_198,
Callithrix jacchus	ENSCJAG00000001431	4 retrocopies	retro_cjac_1073, retro_cjac_2542, retro_cjac_2697, retro_cjac_486,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Felis catus	ENSFCAG00000031287	1 retrocopy	retro_fcat_1989 ,
Gasterosteus aculeatus	ENSGACG00000002034	1 retrocopy	retro_gacu_13,
Gadus morhua	ENSGMOG00000011950	1 retrocopy	retro_gmor_20,
Macropus eugenii	ENSMEUG00000014082	1 retrocopy	retro_meug_164,
Oryctolagus cuniculus	ENSOCUG00000001877	1 retrocopy	retro_ocun_1834,
Oreochromis niloticus	ENSONIG00000017737	1 retrocopy	retro_onil_21,
Sarcophilus harrisii	ENSSHAG00000016107	1 retrocopy	retro_shar_36,
Tetraodon nigroviridis	ENSTNIG00000011331	1 retrocopy	retro_tnig_32,
Takifugu rubripes	ENSTRUG00000003783	1 retrocopy	retro_trub_8,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,