RetrogeneDB ID: retro_fcat_120

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E2:7661715..7663296(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000016301
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NUP62CL
• Ensembl ID: ENSFCAG00000001984
• Aliases: None
• Description: nucleoporin 62kDa C-terminal like [Source:HGNC Symbol;Acc:25960]

Sequence

>retro_fcat_120
ATGAGCGGGTTTAATTTTGGAGGCACTGGGGCCCCCACAGGCGGGTTCACGTTTGGCACCGCAAAGACGGCAACAACCAC
GCCTGCTACCGGCTTCTCTTTCTCTACGTCTGGCACTGGCGGGTTTAACTTTGGGACTCCCTCCCAGCCAGCTGCAAGCA
CCCCTTCTACTGGCCTGTTCTCGCTCACCACCCAAGCTCCAGCGACACAGACCCCAGGGTTCAGTTTTGGAACCACAACT
CCTGCTACGGGAGGAACGGGATTCTCCTTAGGGATCAGCGCTCCGAAGCTAAACCTGAGCAATGCAGCCGCCACCCCAGC
CACTGCTCACCCTGGCGGCTTTGGGCTCGGCGGCAGCACCCTCACCAACGCCATCTCGAGCACTGTCACCTCCAGCCAGA
GCACAGCACCCGCTGGCTTTGTGTTCGGCTCCACCACCACCTCTGCCGCTCCGTCCACCACACCGGGGGGATTCTCGTTC
ACAGGCGGAAGCACGTCCCAGAGCGGGACCTCCGGTTTCAATATTGGCTCCATGGGGAGTTTGGCCCAGCCCACGGCACT
GGGCGGACTGCCCTTCACTCCCGCCACGCCGGCAACCACTGGAGCAGGAGCCACTCAGCCAGCTGCTCCTGCACCTGCCG
CGGCCACCACCAGTGCCGGGCCCACGCTGTTCGCCTCGCTAGCGACCGCTCCAGCCTCCTCCACCACCACCGGGCTTTCC
CTTTGTACCCCGTCAACCACAGCTGCGGCACCCGGGGCCGGAACGCTGGGCTTCAGCTTAAAGGCCCCCGGGGCGGCTTC
TACCTCCTCCACGACAACATCCACTGCCACTGCCACCACTGCCACAGCCACCACCACGGCGGCCACCACCACCGCCGGCT
TTGCCTTGAATCTGAAGCCACTGGCACCGGCCGGGATCGCCAGCAACGCACCGGCTGCCGCGACTGTGCCTCCTGGCTCC
GGTGCACCCACGGGGGCGTCCGCCAGTCCCGTGATGACCTACGCCCAGCTGGAGAGTCTGATCAATAAGTGGAGCCTGGA
GCTGGAGGACCAGGAGCGGCACTTTTTGCAGCAGGCCACACAGGTCAACGCCTGGGACCGCACGCTGATCGAGAATGGGG
AGAAGATCACTACCCTCCACCGCGAGGTGGAGAAAGTGAAGCTGGACCAGAAGAGGCTGGACCAAGAGCTCGACTTCATC
CTGTCTCAGCAGAAGGAGCTGGAAGACCTGCTGAGCCCGCTGGAGGAGTCGGTCAAGGAGCAGAGCGGGACCGTCTACCT
GCAGCACGCCGACGAGGAGCGCGAGAAAACCTACAAGCTCGCCGAGAACATCGACGCGCAGCTGAAGCGCATGGCCCAAG
ACCTCAAGGACATCATCGAGCACCTGAACACGTCTGGAGGTCCCGCCGACACCAGCGACCCCCTGCAGCAGATCTGCAAG
ATCCTCAACGCGCACATGGACTCGCTGCAGTGGATCGACCAGAACTCGGCCCTGCTGCAGAGGAAGGTGGAGGAGGTGAC
CAAGGTGTGCGAGGGGCGTCGCAAAGAGCAGGAGCGCAGCTTCCGGATCACGTTCGACTGA

Alignment

ORF - retro_fcat_120 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.43 %
• Parental protein coverage: 78.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GALGLGTSTLTNSLTSSVPSHWVTA-SSFVFGSATTSAAQSATATGFLFLSGK--KTGRASFSTVSAMEN
          G..GLG.STLTN...S.V.S...TA...FVFGS.TTSAA.S.T..GF.F..G.....G...F.....M..
Retrocopy GGFGLGGSTLTNAISSTVTSSQSTAPAGFVFGSTTTSAAPSTTPGGFSFTGGSTSQSGTSGFN-IGSMGS

Parental  AAQPIAFAGLPLTPTVIISELFGNNQKGSASASTADATTRSSTMLFTSVSDASTSTVASGFSFVSPTTSN
          .AQP.A..GLP.TP........G..Q...A....A.ATT.....LF.S...A..S....G.S...P.T..
Retrocopy LAQPTALGGLPFTPATPATTGAGATQP--AAPAPAAATTSAGPTLFASLATAPASSTTTGLSLCTPSTTA

Parental  GAFGGLTLGFGFKFPGMGGGAHTVSTTASTTTTTTVTTTTTTTTTTSGFTLNLRSLASAGINSIVPVGIN
          .A.G..TLGF..K.P...G.A.T.STT.ST.T.TT.T.TTT..TTT.GF.LNL..LA.AGI.S..P....
Retrocopy AAPGAGTLGFSLKAP---GAASTSSTTTSTATATTATATTTAATTTAGFALNLKPLAPAGIASNAPAAAT

Parental  SIPFTST-VNAIVTPVMTYGQLEGLINEWSLDLEDQERYFLHQATQVNAWDRTLIENGEKITTLHGEVEK
          ..P.......A...PVMTY.QLE.LIN.WSL.LEDQER.FL.QATQVNAWDRTLIENGEKITTLH.EVEK
Retrocopy VPPGSGAPTGASASPVMTYAQLESLINKWSLELEDQERHFLQQATQVNAWDRTLIENGEKITTLHREVEK

Parental  VKLDQKRLEQELDFILSQQKELEDLLTPLEEFVKDQNGAAYLQHEDAEPRKTYKLAENIDAQLKRMAQDL
          VKLDQKRL.QELDFILSQQKELEDLL.PLEE.VK.Q.G..YLQH.D.E..KTYKLAENIDAQLKRMAQDL
Retrocopy VKLDQKRLDQELDFILSQQKELEDLLSPLEESVKEQSGTVYLQHADEEREKTYKLAENIDAQLKRMAQDL

Parental  KDIIENLNTFGSPADVTDRVQQICKILNAHMDFLQWINENSGMLQRKVEEVTQVFEDHHHMELERSVKIA
          KDIIE.LNT.G.PAD..D..QQICKILNAHMD.LQWI..NS..LQRKVEEVT.V.E.....E.ERS..I.
Retrocopy KDIIEHLNTSGGPADTSDPLQQICKILNAHMDSLQWIDQNSALLQRKVEEVTKVCEG-RRKEQERSFRIT

Parental  FD
          FD
Retrocopy FD

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	8.38 RPM	2.41 RPM
SRP017611_kidney	5.67 RPM	0.31 RPM
SRP017611_liver	2.73 RPM	0.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_120 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_120 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017963	1 retrocopy	retro_cfam_218,
Dasypus novemcinctus	ENSDNOG00000001467	1 retrocopy	retro_dnov_1108,
Felis catus	ENSFCAG00000001984	1 retrocopy	retro_fcat_120 ,
Macropus eugenii	ENSMEUG00000001005	1 retrocopy	retro_meug_1130,
Nomascus leucogenys	ENSNLEG00000013865	1 retrocopy	retro_nleu_2076,
Pteropus vampyrus	ENSPVAG00000001787	1 retrocopy	retro_pvam_694,
Vicugna pacos	ENSVPAG00000003649	1 retrocopy	retro_vpac_448,