RetrogeneDB ID: retro_fcat_1770

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F1:14049307..14051383(-)
• Located in intron of: ENSFCAG00000013529

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000010021
• Aliases: None
• Description: None

Sequence

>retro_fcat_1770
AGGGCCGAGACGCATCCTCCGCCCGCAGCAGCCATGAGCACCCCAGCAGTGCCCCGGGAGCTACAACTGCCCCCGAGCCA
GAGGGCCCAGCCCAAGTTCAGAGAACAAAGAAGACAGAAACTCAAGGAACTTATGTTAAAAAGAAAAACGTTTTTTGCAT
ACAAGGAGGAAAATCACATAGCCAGTAGAGACCAGAAAGTGATGACCTCTGAGGGCCAGGTCCACGAAGAGACAAAAGTT
CTGAAATTTAAAACAAAAATGGCTGGTAAAGAAAATGTCAGTAGACCTCCCGGGAGCAAAAATAATGTAACAATGGAAAA
AATTGTATTCCTTTAAGGCCTCCTAATGAACTAACCAATTCAACTATAGCAATTGATACACCTAATTCTGAGGATAATAA
TCAAACTGGGCAGTTGGTACCAATTAAAGGTGACCCTCCAAGGTCAACACATGACATTAAGCCAAGTGTTTCATCTTAAG
AACAACAATAAAAAGAAACAAATAATGACAGAAAAGCCAAAGCAAGATGCTAACATGTCCAAGAAGCTTGTGCGTGGATC
TTACCATGGCCAAATTGTTCAGTCTAAGGTTAATTCATTTAGAAAGCCTCTACAAATCAGAGATGAGAGTTCTGCAGCAA
TAAAGAAACTTTCGACTACAGTCCCTAAAGCTACAGAGCCTCTGCGCACAAACAGCAGCAGTGTGACAGCGAAAAGCAAT
AGAGCCTCTAACGTGATGACTACCACTAAACTTGTGAGCACTACAATTAAGAACAGACAGCTTCTGCGACCTCCTATTAG
AAGTCACCGCGACAATGCTCAGGACGCTGTGAGACCAGGCATCGGTAGAAGCTCGGCCAATGTTACGATTCGGAAAGGAC
CTCACGAGAAAGAGTTAGTGCAATTAAACACAGTTTCATCTAGTGCCAAAACAGGTTCTCAGGATATAGAAAGAAAGAAG
ACACTAACAAGAAGCGTGAAGTCTGAAATCGTAGCCAGGCCTGTTTCATCTTCTAACACCAAACTGATAGAAAAGTCGAA
AAACGTTGACCCTCGCAGGCATACAATAGCAAAAGCAACTGTTGATAGATCAGCTCAGCCCAAAGAAACAGCAGAAGAGA
GAAAAGCTCGTCTGAGTGAGTAGAAAGCTGGCAAAAGGAAAGTCCTGAAAAGGCCTCCTAGCTCAGGAGTTACCCAGCCG
GAGCCTGAAGGGCAACACGAAAACCCAGTTGGGTCCTTTTGGACTACCATGGTAGAAGAAGATGAACAAAGATTATTTAC
CGAAAAAGTGAACAAGACATTTTCTGAATGCCTAAACCTGATTAGTGAGGGATGCCCAAAAGAAGAAATATTGGTCATAC
TGAGTGACCTGATTAAAAATATTCTGGATGCCAAAAAGCTTGTTAAATATTGGATATGCCTTGCACGTATTGAACCACTC
ACAAGTCCTATTGAAAACATTATCACAATCTATGAGAAAGCCATTCTGGCGGGCGCTCAGCCTATTGAAGAGATGCGACA
TACCATAGCAGATATTCTGACAATGAAGAGTCAAGAAAAAGTTAAATATGGAGAAAATGTTGAGGAGGCTTGTGCAACCA
AGGAATACATCCATGAAGTCAGCACTGAAGATAGAGGGGTTAATCTAGAGTCAGGAAAACCAGAAATGGAAAAGAAAACT
AGAAATGTGGTATTCCAGGATGATGAAAAAGAGCAAGATGACAAAACAAACGATTCAACCAATGATGTTAAAACCCCCAG
TACAGAAACCAGGGGGAGTTGCTTAATTAAATATAATGTGTCTACTACACCATACCTACAAAGTGTAAAAAAGAAGATAC
AGTTTGACAATACAGATTCTACATTTAAAGAGCTAAAGTTTCTAACACCAGTGAGACATTCTCGACGTATTCAAGAGAAG
ACTTCTAAATTGCCAGATATGTTAAAAGACCATTATCCTTGTGTGTCTTCATTGGAACAATTAACAGAGTTGGGAGGTGA
AACTGATGCTTTCGTATGCCGTCCCAATTCAGCACTATGCCCGATGTTCTCAGAGCCTGGAACAGCAGAAGAGAAA

Alignment

ORF - retro_fcat_1770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RAETRPPPAAAMSTPAVPRELQLPPSQRAQPEFREQRRQKLKEHMLKRKTFFAYKEENHISRVSRDQKVM
          RAET.PPPAAAMSTPAVPRELQLPPSQRAQP.FREQRRQKLKE.MLKRKTFFAYKEENHI...SRDQKVM
Retrocopy RAETHPPPAAAMSTPAVPRELQLPPSQRAQPKFREQRRQKLKELMLKRKTFFAYKEENHIA--SRDQKVM

Parental  TLTSEGQVHEETKVLKFKTKMAGKENVSRPPGSKNNVTMEK-NCIPLRPSNELTNSTIAIDTPNSEDNNQ
          T..SEGQVHEETKVLKFKTKMAGKENVSRPPGSKNNVTMEK.NCIPLRP.NELTNSTIAIDTPNSEDNNQ
Retrocopy T--SEGQVHEETKVLKFKTKMAGKENVSRPPGSKNNVTMEK<NCIPLRPPNELTNSTIAIDTPNSEDNNQ

Parental  TGQLVPIKGDPP-GQHMTLSQVFHLKNNNKKKQIMTEKPKQDANISKKLVLGSYRGQIVQSKINSFRKPL
          TGQLVPIKGDPP.GQHMTLSQVFHLKNNNKKKQIMTEKPKQDAN.SKKLV.GSY.GQIVQSK.NSFRKPL
Retrocopy TGQLVPIKGDPP>GQHMTLSQVFHLKNNNKKKQIMTEKPKQDANMSKKLVRGSYHGQIVQSKVNSFRKPL

Parental  QIRDESSAAIKKLSTAVPKATEPLHTNSSSVTAKSDRASNVTTTTKLVSTTIQNRQLLRPPIRSHHDNAQ
          QIRDESSAAIKKLST.VPKATEPL.TNSSSVTAKS.RASNV.TTTKLVSTTI.NRQLLRPPIRSH.DNAQ
Retrocopy QIRDESSAAIKKLSTTVPKATEPLRTNSSSVTAKSNRASNVMTTTKLVSTTIKNRQLLRPPIRSHRDNAQ

Parental  DAVRPGIGRSSANVTMRKGPREKELVQLNTVSSSAKTGSQDIERKKTLTRSVKSEIVARPVLSSNTKLIE
          DAVRPGIGRSSANVT.RKGP.EKELVQLNTVSSSAKTGSQDIERKKTLTRSVKSEIVARPV.SSNTKLIE
Retrocopy DAVRPGIGRSSANVTIRKGPHEKELVQLNTVSSSAKTGSQDIERKKTLTRSVKSEIVARPVSSSNTKLIE

Parental  KSKNVDPRRHTIAKATIDRSAQPKETAEERKARLSEWKAGKRKVLKRPPSSGVTQPEPEGQHKNPVGSFW
          KSKNVDPRRHTIAKAT.DRSAQPKETAEERKARLSE.KAGKRKVLKRPPSSGVTQPEPEGQH.NPVGSFW
Retrocopy KSKNVDPRRHTIAKATVDRSAQPKETAEERKARLSE*KAGKRKVLKRPPSSGVTQPEPEGQHENPVGSFW

Parental  TTMVEEDEQRLFTEKVNKTFSECLNLISEGCPKEEILVILNDLIKNIPDAKKLVKYWICLARIEPLTSPI
          TTMVEEDEQRLFTEKVNKTFSECLNLISEGCPKEEILVIL.DLIKNI.DAKKLVKYWICLARIEPLTSPI
Retrocopy TTMVEEDEQRLFTEKVNKTFSECLNLISEGCPKEEILVILSDLIKNILDAKKLVKYWICLARIEPLTSPI

Parental  ENIITIYEKAILAGAQPIEEMRHTIADILTMKSQEKKCISIGENIEEACATKEYIHEVSTEDRGVNLESG
          ENIITIYEKAILAGAQPIEEMRHTIADILTMKSQEK.....GEN.EEACATKEYIHEVSTEDRGVNLESG
Retrocopy ENIITIYEKAILAGAQPIEEMRHTIADILTMKSQEK--VKYGENVEEACATKEYIHEVSTEDRGVNLESG

Parental  KPEMEKKTRNVVFQDDEKEQDDKTNNSTNDVKTPSTETRGSCLIKYNVSTTPYLQSVKKKIQFDNTDSTF
          KPEMEKKTRNVVFQDDEKEQDDKTN.STNDVKTPSTETRGSCLIKYNVSTTPYLQSVKKKIQFDNTDSTF
Retrocopy KPEMEKKTRNVVFQDDEKEQDDKTNDSTNDVKTPSTETRGSCLIKYNVSTTPYLQSVKKKIQFDNTDSTF

Parental  KELKFLTPVRRSRRIQEKTSKLPDMLKDHYPCVSSLEQLTELGGETDAFVCRPNSALCPMFSEPGTAEEK
          KELKFLTPVR.SRRIQEKTSKLPDMLKDHYPCVSSLEQLTELGGETDAFVCRPNSALCPMFSEPGTAEEK
Retrocopy KELKFLTPVRHSRRIQEKTSKLPDMLKDHYPCVSSLEQLTELGGETDAFVCRPNSALCPMFSEPGTAEEK

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	5.16 RPM	2.07 RPM
SRP017611_kidney	3.09 RPM	1.44 RPM
SRP017611_liver	1.72 RPM	0.61 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1770 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1770 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005898	1 retrocopy	retro_cfam_968,
Choloepus hoffmanni	ENSCHOG00000009905	2 retrocopies	retro_chof_1493, retro_chof_973,
Cavia porcellus	ENSCPOG00000012382	1 retrocopy	retro_cpor_171,
Felis catus	ENSFCAG00000010021	1 retrocopy	retro_fcat_1770 ,
Felis catus	ENSFCAG00000028904	1 retrocopy	retro_fcat_615,
Myotis lucifugus	ENSMLUG00000000132	1 retrocopy	retro_mluc_1515,
Monodelphis domestica	ENSMODG00000010436	1 retrocopy	retro_mdom_1364,
Mustela putorius furo	ENSMPUG00000017996	1 retrocopy	retro_mputfur_1270,
Mus musculus	ENSMUSG00000037725	1 retrocopy	retro_mmus_2651,
Otolemur garnettii	ENSOGAG00000008428	1 retrocopy	retro_ogar_1743,
Tupaia belangeri	ENSTBEG00000005807	1 retrocopy	retro_tbel_176,
Tursiops truncatus	ENSTTRG00000009624	2 retrocopies	retro_ttru_1491, retro_ttru_1741,