RetrogeneDB ID: retro_fcat_43

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D2:5519303..5521235(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000028055
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSTF2
• Ensembl ID: ENSFCAG00000007000
• Aliases: None
• Description: cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa [Source:HGNC Symbol;Acc:2484]

Sequence

>retro_fcat_43
ATGTCGAGTTTAGCGGTGAGAGACCCGGCGATGGATCGGTCACTGCGTTCCGTGTTCGTGGGGAACATTCCGTATGAGGC
AACCGAGGAGCAGCTGAAGGACATTTTCTCGGAGGTCGGTTCTGTGGTCAGTTTCCGGCTGGTGTACGACCGGGAGACGG
GCAAGCCCAAGGGCTATGGCTTCTGCGAGTACCAGGACCAGGAGACCGCGCTGAGCGCCATGCGCAACCTCAACGGGCGC
GAGTTCAGCGGCCGGGCGCTGCGGGTGGACAACGCGGCCAGCGAGAAGAACAAGGAGGAGCTCAAGAGCCTGGGGCCCGC
GGCGCCCATCATCGACTCGCCCTACGGGGACCCCATCGACCCGGAAGACGCCCCCGAGTCCATCACCAGGGCGGTCGCCA
GTCTGCCCCCCGAGCAGATGTTCGAGCTCATGAAGCAGATGAAGCTGTGCGTGCAGAACAGCCACCAGGAAGCGCGAAAT
ATGCTGCTTCAGAACCCCCAGCTGGCCTATGCGCTGCTGCAGGCCCAGGTGGTGATGAGAATAATGGACCCGGAGATTGC
TCTGAAAATCCTGCACCGCAAGATCCACGTCACCCCGCTCATCCCGGGCAAGTCTCAGCCCGTGTCCGGCCCCGGCCCCG
GCCCCGGCCCGGGGCTGTGCCCGGGACCCAGTGTCCTGCTGAACCAGCAGAACCCGCCAGCCCCTCAGCCGCAGCATATG
GCCAGACGGCCAGTGAAAGACATTCCTCCTCTGATGCAGACCCCTATCCAGGGCGGGATCCCAGCCCCGGGGCCGATGCC
AGCTGCGGTTCCCGGACCCGGGCCTGGTTCCCTAACTCCCGGGGGAGGCATGCAGCCCCAGGTTGGGATGCCGGGCGTCG
GCCCAGTGCCTTTAGAGCGGGGACAGGTGCAGATGTCGGATCCCCGAGCTCCTCTACCTCGTGGACCCATGACTGCCGGT
GGCCTGCCTCCTCGAGGGCTGTTAGGAGATGCTCCAAACGACCCCCGTGGAGGGACTTTGCTTTCAGTCACCGGGGAGGT
AGAGCCCAGAGGCTATCTTGGCCCACCTCATCAGGGCCCCCCCATGCACCACGCCTCTGGTCACGACGGCCGGGGCCCTT
CCTCCCATGAGATGAGGGGAGGGCCATTAGCAGATCCCAGACTGCTAATTGGAGAGCCCAGAGGACCCATGATAGATCAA
AGGGGTCTCCCAATGGATGGTAGAGGAAGTAGAGATTCTCGAGGGATGGAGACTCGAGCCATGGAGACGGAAGTCTTGGA
GACCCGAGTAATGGAGAGAAGAGGAATGGAGACCTGTGCAATGGAAACCAGAGGGATGGAAGCGAGAGGCATGGATGGAA
GAGGAATGGAGCTAAGGGGCCCTGGCCCCAGCTCCAGAGGCCCTATGACTGGTGGAATCCAGGGTCCTGGTCCCATTAAT
ATGGGGGCAGGTGGTCCTCAGGGACCCAGACAGGTCTCGAGCATTTCAGGGGTGGGAAATCCTGGAGCGGGCATGCAGGG
GGCAGGCATACAAGGAACGGGCATGCAGGGGGCGGGCATACAAGGAACGGGCATGCAGGGGGCGGGCATACAAGGAACGG
GCATGCAGGGGGCGGGCATACAAGGAACGGGCATGCAGGGGGCGGGCATACAAGGAACGGGCATGCAGGGGGCGGGCATA
CAAGGAGCAGGCATGCAGGGGGCGGGCATACAAGGAGTGGGCATGCAGGGGGCGGGTAAGCAAGGTGGAGGCCAGCCGAG
CAGTTTTAGCCCTGGGCAGAGCCAGGTAACTCCGCAGGATCAAGAGAAGGCAGCTCTGATCATGCAGGTTCTCCAACTGA
CTGCAGATCAGATCGCCATGCTGCCTCCTGAGCAAAGGCAGAGCATCCTGATTTTAAAGGAACAAATTCAGAAATCTACT
GGAGCTTCTTGA

Alignment

ORF - retro_fcat_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.12 %
• Parental protein coverage: 84.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGLTVRDPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA
          M..L.VRDPA.DRSLRSVFVGNIPYEATEEQLKDIFSEVG.VVSFRLVYDRETGKPKGYGFCEYQDQETA
Retrocopy MSSLAVRDPAMDRSLRSVFVGNIPYEATEEQLKDIFSEVGSVVSFRLVYDRETGKPKGYGFCEYQDQETA

Parental  LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVIESPYGETISPEDAPESISKAVASLPPEQM
          LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLG..AP.I.SPYG..I.PEDAPESI..AVASLPPEQM
Retrocopy LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGPAAPIIDSPYGDPIDPEDAPESITRAVASLPPEQM

Parental  FELMKQMKLCVQNSPQEARNMLLQNPQLAYALLQAQVVMRIVDPEIALKILHRQTNIPTLIAGNPQ----
          FELMKQMKLCVQNS.QEARNMLLQNPQLAYALLQAQVVMRI.DPEIALKILHR......LI.G..Q....
Retrocopy FELMKQMKLCVQNSHQEARNMLLQNPQLAYALLQAQVVMRIMDPEIALKILHRKIHVTPLIPGKSQPVSG

Parental  PVHSAGPG--SGSSVSMSQQNPQAPQAQSLGGMHVNGAPPLMQASMQAGVPAPGQIPATVTGPGPGSLAP
          P....GPG...G.SV...QQNP.APQ.Q......V...PPLMQ...Q.G.PAPG..PA.V.GPGPGSL.P
Retrocopy PGPGPGPGLCPGPSVLLNQQNPPAPQPQHMARRPVKDIPPLMQTPIQGGIPAPGPMPAAVPGPGPGSLTP

Parental  GGGMQAQVGMPGSGPVSIERGQVPMQDPRAAMQRGPLPANVPTPRGLLGDAPNDPRGGTLLSVTGEVEPR
          GGGMQ.QVGMPG.GPV..ERGQV.M.DPRA...RGP..A....PRGLLGDAPNDPRGGTLLSVTGEVEPR
Retrocopy GGGMQPQVGMPGVGPVPLERGQVQMSDPRAPLPRGPMTAGGLPPRGLLGDAPNDPRGGTLLSVTGEVEPR

Parental  GYLGPPHQGPPMHHVPGHDSRGPPPHEMRGGPLAEPRPLMAEPRGPMLDQRGPPLDGRGGRDPRGIDTRG
          GYLGPPHQGPPMHH..GHD.RGP..HEMRGGPLA.PR.L..EPRGPM.DQRG.P.DGRG.RD.RG..TR.
Retrocopy GYLGPPHQGPPMHHASGHDGRGPSSHEMRGGPLADPRLLIGEPRGPMIDQRGLPMDGRGSRDSRGMETRA

Parental  MEARAMEARGLDARGLEARAMEARAMEARAMEARAMEARAMEVRGIEARSMDTRGPVPGPRGPIPSGIQG
          ME....E.R....RG.E..AME.R.MEAR.M..R.ME.R.....G...R...T.G...GP.GPI..G..G
Retrocopy METEVLETRVMERRGMETCAMETRGMEARGMDGRGMELRG---PGPSSRGPMTGG-IQGP-GPINMGAGG

Parental  P
          P
Retrocopy P

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	16.76 RPM	10.79 RPM
SRP017611_kidney	8.55 RPM	9.38 RPM
SRP017611_liver	6.27 RPM	7.38 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_43 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_43 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009325	1 retrocopy	retro_ecab_19,
Felis catus	ENSFCAG00000007000	1 retrocopy	retro_fcat_43 ,
Macropus eugenii	ENSMEUG00000011186	1 retrocopy	retro_meug_356,
Tursiops truncatus	ENSTTRG00000013556	1 retrocopy	retro_ttru_1363,