RetrogeneDB ID: retro_fcat_583

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:156235684..156236664(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSFCAG00000031631
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]

Sequence

>retro_fcat_583
CAGCCATGGCCAATAGTTCTACAAGGAAAAGATCTTATAGGATTAGCCCAAACTGGAACAGGGAAGACTGTCCTACTTAG
TGCCTGGATTATCCATCTTGATTTACAGCCCATAATTAGAGAAAAAAAGAACGGACCCAGAATGTTAGTTCTTACACCCA
CTAGGTAATTAGGTCTTCATGTGGAAGCAGAATGTTCTATGTATTCGTATAAAGGCCTTAAAAGTGTTTGTATATATGGT
AGTGGAGATAGAAATGGAAAAATACAATAACTGAAAAAAGGAGTAGATATTATTGTAACTCCTGGAAGACTGAATGATTT
ACAAATGAGTAACTGTTCCAATCTCAGAAGCATAACCTACTTGGTATTAGATGAAGTCGACAAGAAGCTAGACATGGGAT
TTGACCCCAGATAATAACGATTTTATTAGATGTGCACCAGACAGGCAGACTATTATGACAAGTGCAACGTGGTCATATGC
TGTCCGTGAACTTGCACAATTTTATTTGAAAAAGCCAATGATTGTATATGTTGGTACATTGGATCTTGTTGCTGTAAGTA
CCATGAAACAAAACGTAATTGTCACCACAGAAGAAGAGAAATGATCTCATATCCAAGTGTTTTTAGAAAACTTGTCTCCC
AAGGACAAAGTCATAATGTTTGTCAGCAGAAAAGTTTGCTCATCAAGTGACCCAATTCTGCGACATGGATTGGTGGGAGT
CCCTTCACGGCGACAGAAAACAGATGGCCAAGAGAGAACATTAGAAAAGTTTAAAACAGGTAGAGTAAGAATATTGATTG
CTTCAGATTTGACATCTTGAGGTCTCAATGTCCACGATATCACACATGTCTATAATTATGATTTCCCTGGAACATCAAAG
AATGTGTACATAGAGTAGGATGCACTGAAAGAGCAGGGAGGACTTAACATCCACTACCCTCATCACTAGAAATGACTGGA
GGGTTGCTGGTGAGTTAATA

Alignment

ORF - retro_fcat_583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.78 %
• Parental protein coverage: 51.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  QTWPIVLQGIDLIGVSQTGT-GKTLSYLMPGF-IHLDLQPVIREKRNGPGMLVLIPTRELALQVQVECSK
          Q.WPIVLQG.DLIG..QTGT.G..LSYL.PG..IHLDLQP.IREK.NGP.MLVL.PTR.L.L.V..ECS.
Retrocopy QPWPIVLQGKDLIGLAQTGT>GR-LSYLVPGL<IHLDLQPIIREKKNGPRMLVLTPTR*LGLHVEAECSM

Parental  YSYKGLKSVCIYGGGDRNGQIQELKKGVDIIIATPGRLNDLQMNNFVDLRSITYLVLDEADKMLDMGFEP
          YSYKGLKSVCIYG.GDRNG.IQ.LKKGVDII..TPGRLNDLQM.N...LRSITYLVLDE.DK.LDMGF.P
Retrocopy YSYKGLKSVCIYGSGDRNGKIQ*LKKGVDIIV-TPGRLNDLQMSNCSNLRSITYLVLDEVDKKLDMGFDP

Parental  -QIMKILLDVR-PDRQTIMTSATWPYAVRRLAQSYLKEPMIVYVGTLDLIAVSTVKQNIIVTTEEEKRSH
          .QI..ILLDV..PDRQTIMTSATW.YAVR.LAQ.YLK.PMIVYVGTLDL.AVST.KQN.IVTTEEEK.SH
Retrocopy <QIITILLDVH<PDRQTIMTSATWSYAVRELAQFYLKKPMIVYVGTLDLVAVSTMKQNVIVTTEEEK*SH

Parental  IQTFLENMSPKDKVIVFVSRKAVADHLSSDLILQHISV-ESLHGNREQ-KDREKALENFKTGKIRILIAT
          IQ.FLEN.SPKDKVI.FVSRK......SSD.IL.H..V.ESLHG.R.Q....E..LE.FKTG..RILIA.
Retrocopy IQVFLENLSPKDKVIMFVSRKVCS---SSDPILRHGLV>ESLHGDRKQ<DGQERTLEKFKTGRVRILIAS

Parental  DLGSRGLDVHDITHVYNYDFPR-NIEEYVHRVGRTGRAGKT-GMSITLITRNDWRIAGELI
          DL.S.GL.VHDITHVYNYDFP..NI.E.VHRVG.T.RAG.T...S.TLITRNDWR.AGELI
Retrocopy DLTS*GLNVHDITHVYNYDFPG<NIKECVHRVGCTERAGRT<LTSTTLITRNDWRVAGELI

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_583 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_583 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.

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007851	1 retrocopy	retro_amel_31,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Equus caballus	ENSECAG00000017971	1 retrocopy	retro_ecab_7,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583 ,
Homo sapiens	ENSG00000080007	1 retrocopy	retro_hsap_76,
Gorilla gorilla	ENSGGOG00000016092	1 retrocopy	retro_ggor_2889,
Microcebus murinus	ENSMICG00000017145	1 retrocopy	retro_mmur_1603,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14,
Mustela putorius furo	ENSMPUG00000004342	1 retrocopy	retro_mputfur_47,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Oryctolagus cuniculus	ENSOCUG00000006338	2 retrocopies	retro_ocun_1061, retro_ocun_227,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,