RetrogeneDB ID: retro_fcat_1273

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:64053969..64055830(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIG3
• Ensembl ID: ENSFCAG00000000249
• Aliases: None
• Description: ligase III, DNA, ATP-dependent [Source:HGNC Symbol;Acc:6600]

Sequence

>retro_fcat_1273
TTGGCTTTCAAGATCCTCTTCCCACCAAAGCTCCCTGCACTCAGCTGTAAAGAACTGTGCATATTCTGAGAACAACATCA
TTGGTCTGACATAAGACAATTCAGCCACTGGTCACAAACAAATCTGTTTCATGGGCAGAGATGAAAGCCTGTTCTGTCAT
TCCAGGAAGGTAATCTAAGACCACGTGCTACCTGCCTTATTTTCTTGCCAAAGTTGCATGTGGGACTCTGCAGCAGCCCG
TGAGATGGCTGAACAATGGCTCTGTGTGGACTATGCCAAGCGTGGCATGGCTGGCTGCAGAAAACGCAAGGAAAAGATTG
TGAAAAGTGTATGCTGGATCAGCAAAGTGGTGCTCAATCCTTTTCAGAGTCCAGCAGGAATATGAAGAAGTGGTATCACA
TTTAAAAATGCACATTTGAGAAACTGGAGTGGACCAAGGCTGCCACAAAAAGTACTGATGACCTTACAAGCTGGAAGGCT
GGGAGAAGCTGGAAGATAATGAGAAGGAACAGATAAGCCAACACATTGTAGATCTGTCTTCTAAGGCAATAAGCACACCA
AAGAAAGCTGTTGTCCAGGCTAAGATGACAGCCACTGGCCAGGTGACATCTCCAATGAAAGGTACCTCATTTGTCATCAA
TATCAATCCCCAGAAATTTTCTGGTTTTTCATCCAAGCCCACCAACTCTGGGGAAGCCCACTTGAGCTTGACCCCTAAGG
CAAGTCTGTCCTCAAGCAAATGGGATCCCCAGCACAAGGATGATCTGCTACGTGAGTTTTGGAAGTTGTGCACCATTGTG
GCTGAAAATCCTTGCTATAATAGGATGACCCAGATCATCCAGAACTTCCTTTGGAAAAGTTTGGCAGGAGATGGTTTCCA
CAGTGACGTGTACCTAAAAGTTAAGCTGCTGCTGCCAGGTGTTATTAGGAGTATTTGCAACTTAAATAATAAGCAGACTG
TAAAGCTTTTCAGCCTAACTTTGCACTGCAACCCAAATGATATGGCATGAGACCTAGAGCAGGTTAGGTATCAGAGACAA
CCAGAATCTTCTTTGAGCAGAGCAAGTCTGTCCTCCCAGGTGCCAAGAGTCTCCTTAACATCCAAGAGGTGGACAACTTC
CTCCTTCAGCTCTCCAAGCTCACCAAGGAGAATGAGCAGCAACAGGCCCTGCAGGACACTGCCTCCAGGTACACAGCCAA
TGACCTTAAGTGCATCATCAAGTTGATCAAACATAACCCAAGGATGAACTTGGGTGCAAAACATGTGTTCAATGCCCTTG
ACTCCTGTTGCCTATAAAGCATCACACAACCTGCAGGACGTGGTGTAGCAGGTCCTCTGCAATGAGCAGGAGGTGGAGAA
GGAGCCAGGCCAGAGATAAGCTCTGAGCATCCAGCCATCACTGATGATGCCAGTGCAGCCCTTGCTGGCTGAGGCCTGCA
AGTCCATCAAGCATGTGATAAAGACATGCTCTAATGGCATGCTGTCTAAAATTAAGTATGATGCGGAGTGAGTCCAGGAG
CATAATAATGGGGACCACTTCAGCTACTTCAGCCGCATATTGAATCCTGTCTTGCCTCACAAGGTGGCCCACCTTAAGGA
CTACATCCACCAGGCTTTCCCTGGGGGCACAACATGATCTTAGACTTTGAGGTGCTCCTGATCAACACTAGGACAGCCAA
ACTTCTGCCCTTTGGGATTCCTGGAGTGCGTAAGAAAGCTGCCTTCCAGGATGCTAATGTCTGCCTGTTTGTTTTTTATT
TTACCTACTTCAATGTCAAGTTGAAGGACAGGCCTCTGTGCAAGCAGCAGAAGTTTCTTCATGATAACATGGTTGAAATT
CCCAACCAGATCATGTTCTCA

Alignment

ORF - retro_fcat_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.57 %
• Parental protein coverage: 62.19 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LTFKILFLPTLRALGRKELCLFGEQHRWPDRRQFSHWSETELFHGHGLLQRRKAVLSSQKGGLRPRATRL
          L.FKILF.P.L.AL..KELC.F.EQH.W.D.RQFSHWS.T.LFHG....QR.K.VLS.Q.G.LRPRAT.L
Retrocopy LAFKILFPPKLPALSCKELCIF*EQHHWSDIRQFSHWSQTNLFHG----QR*KPVLSFQEGNLRPRATCL

Parental  V-FLPGSHVGLCSGPC-EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPF-SESGGDMKEWY
          ..FL.....G....P..EMAEQ..CVDYAKRG.AGC.K.KEKIVK.VC.I.KVV.NPF.SES...MK.WY
Retrocopy I<FLAKVACGTLQQPV<EMAEQWLCVDYAKRGMAGCRKRKEKIVKSVCWISKVVLNPF<SESSRNMKKWY

Parental  HI-KCMFEKLERARATTKKIEDLT-ELEGWEELEDNEKEQISQHIADLSSKATSTPKKKAVVQAKLTATG
          HI.KC.FEKLE...A.TK...DLT..LEGWE.LEDNEKEQISQHI.DLSSKA.STPKK.AVVQAK.TATG
Retrocopy HI*KCTFEKLEWTKAATKSTDDLT<KLEGWEKLEDNEKEQISQHIVDLSSKAISTPKK-AVVQAKMTATG

Parental  QVTSPVKGASFVTNTNPRKFSGFAAKPNNSGEARSSPTPKASLSSSRCDPKHKDCLLREFRKLCAMVAEN
          QVTSP.KG.SFV.N.NP.KFSGF..KP.NSGEA..S.TPKASLSSS..DP.HKD.LLREF.KLC..VAEN
Retrocopy QVTSPMKGTSFVININPQKFSGFSSKPTNSGEAHLSLTPKASLSSSKWDPQHKDDLLREFWKLCTIVAEN

Parental  PSYNTKTQIIQDFLRKGSAGDGFHGDVYLTVKLLLPGVIKSVYNLNDKQIVKLFSRIFNCNPDDMARDLE
          P.YN..TQIIQ.FL.K..AGDGFH.DVYL.VKLLLPGVI.S..NLN.KQ.VKLFS....CNP.DMA.DLE
Retrocopy PCYNRMTQIIQNFLWKSLAGDGFHSDVYLKVKLLLPGVIRSICNLNNKQTVKLFSLTLHCNPNDMA*DLE

Parental  Q-GDVSETIRVFFEQSKSFPPAAKSLLTIQEVDAFLLCLSKLTKEDEQQQALQDIASRCTANDLKCIIRL
          Q.G.VSET.R.FFEQSKS..P.AKSLL.IQEVD.FLL.LSKLTKE.EQQQALQD.ASR.TANDLKCII.L
Retrocopy Q<G*VSETTRIFFEQSKSVLPGAKSLLNIQEVDNFLLQLSKLTKENEQQQALQDTASRYTANDLKCIIKL

Parental  IKHDLKMNSGAKHVLDALD-PNAYEAFKASRNLQDVVERVLRNEQEVEKEPGRRRALSVQASLMTPVQPM
          IKH...MN.GAKHV..ALD.P.AY...KAS.NLQDVV..VL.NEQEVEKEPG.R.ALS.Q.SLM.PVQP.
Retrocopy IKHNPRMNLGAKHVFNALD>PVAY---KASHNLQDVV*QVLCNEQEVEKEPGQR*ALSIQPSLMMPVQPL

Parental  LAEACKSIEHAMKKCPNGMFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHKVAHFKDYIPQAFPG-GH
          LAEACKSI.H..K.C.NGM.S.IKYD.E.VQ.H.NGDHFSYFSR.L.PVLPHKVAH.KDYI.QAFPG.GH
Retrocopy LAEACKSIKHVIKTCSNGMLSKIKYDAE*VQEHNNGDHFSYFSRILNPVLPHKVAHLKDYIHQAFPG<GH

Parental  SMILDSEVLLIDTKTGKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNDISLMDRPLCERRKFLHDNMVE
          .MILD.EVLLI.T.T.K.LPFG..GV.KKAAFQDANVCLFVF...YFN...L.DRPLC...KFLHDNMVE
Retrocopy NMILDFEVLLINTRTAKLLPFGIPGVRKKAAFQDANVCLFVFYFTYFN-VKLKDRPLCKQQKFLHDNMVE

Parental  IPNRIMFS
          IPN.IMFS
Retrocopy IPNQIMFS

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	32.94 RPM
SRP017611_kidney	0.00 RPM	24.42 RPM
SRP017611_liver	0.00 RPM	15.87 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1273 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1273 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000000249	1 retrocopy	retro_fcat_1273 ,