RetrogeneDB ID: retro_fcat_589

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:165351881..165352650(+)
• Located in intron of: ENSFCAG00000006125

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIF3L1
• Ensembl ID: ENSFCAG00000023186
• Aliases: None
• Description: NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:13390]

Sequence

>retro_fcat_589
GTCCATATTTATTCTCCTCACACAGCCCAGGATGCCGCGCCTCACGAAGTCAGCAGCCAGTTGGCTTAAGGGCTTGGAGT
TTGCACCTCCAGGCCCACACATCCTTCCAAAGCTCCCAACTACCCCACGAGGGGAATGTACAGGGTAGAATTCGGTGTTA
CCTGCACCCACGGACCGGCCAAAGTCATTTCTGCAGTGAAAGGAATTGTGCGTGTTTCTGTCACTTCTTCTACTAGGACT
GGTGATGAAGAACAAACGTGGATTAGTCTGAATTGTAGTCAGGGGGATTTGATGCAGGTGGTGGCTGTTCTTTCTAAGAG
CAGACATTTTATCCGAAGACTGAAATTCTGTCACTGGGGAAGCCTCAGCTCCCACATGCTGGAATGGGACAGTTGTGCAC
GGTGGATGTGTCTGTTTCCTTGGCAGCCATGATTGTGTGAATCAAAAGTCACTTTAAACTATCTCATGGTCGCCTTGCTC
TTGAGGTAAGAAGGATCTTGGTGTCTCCAGTCAAAGCTGTGACCCAGTGCACTGGTTCTAGGAGCACTGTGCTGCAGGTT
GGCAGTGGCCGACCTTTCCCTCACAAGTGAGATGTCCCGTCGTGATGCTCTGTATGCTGCACCCCAAGGAATAAATGTCA
TCCTGTGTCAACACAGCAACATCGAGTGAAGCTTTCTTTCTGATCTTCAAGATATGCTGGGTGCTCCCTTAGGAAAATAA
GATTAATATTATCCTGTCAGAAACAGACAGGGACCCGCTTCATGTGGTG

Alignment

ORF - retro_fcat_589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 68.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VGIYSPHTAYDAAPQGVNSWLAKGLGVCTSRPIHPSKAANYPTGGTHRVEFSVNSTQHLDKVISAVKEIA
          V.IYSPHTA.DAAP..V.S.LA.GLGVCTSRP.HPSKA.NYPT.G..RVEF.V..T....KVISAVK.I.
Retrocopy VHIYSPHTAQDAAPHEVSSQLA*GLGVCTSRPTHPSKAPNYPTRGMYRVEFGVTCTHGPAKVISAVKGIV

Parental  NISITSFSTRTDDEEQTRISLNCSQEALLQVMAFLSQNRQ-FYQKTEILLLEKPPLPQTGMGRLCTLDEP
          ..S.TS.STRT.DEEQT.ISLNCSQ..L.QV.A.LS..R..FY.KTEIL.L.KP.LP..GMG.LCT.D..
Retrocopy RVSVTS-STRTGDEEQTWISLNCSQGDLMQVVAVLSKSRH<FYPKTEILSLGKPQLPHAGMGQLCTVDVS

Parental  ASLATMIERIKRHLKLAHVRLALGVGRTLESPVRVVALCAGSGSTVLQG-VEADLYLTGEMSHHDVLDAA
          .SLA.MI..IK.H.KL.H.RLAL.V.R.L.SPV..V..C.GS.STVLQ....ADL.LT.EMS..D.L.AA
Retrocopy VSLAAMIV*IKSHFKLSHGRLALEVRRILVSPVKAVTQCTGSRSTVLQV>AVADLSLTSEMSRRDALYAA

Parental  SQGINVILCEHSNTERGFLSDLRDMLGAHL-ENKINIILSERDRDPLHVI
          .QGINVILC.HSN.E..FLSDL.DMLGA.L.ENKINIILSE.DRDPLHV.
Retrocopy PQGINVILCQHSNIE*SFLSDLQDMLGAPL>ENKINIILSETDRDPLHVV

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	23.07 RPM
SRP017611_kidney	0.00 RPM	24.42 RPM
SRP017611_liver	0.00 RPM	9.10 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_589 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_589 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 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023186	1 retrocopy	retro_fcat_589 ,
Macaca mulatta	ENSMMUG00000006639	1 retrocopy	retro_mmul_444,
Nomascus leucogenys	ENSNLEG00000006935	1 retrocopy	retro_nleu_1504,
Oryctolagus cuniculus	ENSOCUG00000010667	16 retrocopies	retro_ocun_1105, retro_ocun_1534, retro_ocun_1539, retro_ocun_1691, retro_ocun_1692, retro_ocun_1710, retro_ocun_1729, retro_ocun_1749, retro_ocun_1789, retro_ocun_1828, retro_ocun_1837, retro_ocun_1841, retro_ocun_1846, retro_ocun_1847, retro_ocun_1854, retro_ocun_929,
Pongo abelii	ENSPPYG00000013063	1 retrocopy	retro_pabe_244,
Tupaia belangeri	ENSTBEG00000000704	1 retrocopy	retro_tbel_3512,