RetrogeneDB ID: retro_fcat_277

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:164571978..164572496(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SURF2
• Ensembl ID: ENSFCAG00000028927
• Aliases: None
• Description: surfeit 2 [Source:HGNC Symbol;Acc:11475]

Sequence

>retro_fcat_277
AGACTCACCCTATGGCACATCAACAAGTCCCAGAACATGTGCTGAGGCATCCCCAGGGCCAGCGGTACCAGAGAGCTCTG
CGTGAATATGAAGAGTGTCAGAAGCAGGGTGTGGAGTGTGTGTCTGCCTGCCTCCTTCACAAAAGGAGACCGAGGGAAGA
CCAGACGGACAGCTCCAGGCCACCTCGCCTGAGAGAAGCCTTCTGGGAACCTGCATCCAGCAATGACAATGCAACTGTGA
GTGACAGTGATGACAGCATGACAGACCTCTAACCACCGGAATTGTTCACCAGAAAGGACCTGGGAGGGAATGAGCATGGC
GACAGCACCAATGACTTTTTGACAAAAGAGGAGGACAAGAAGCCATGACACCCAACAGAGAAAGGCCCTGGGGACAGAGA
AGAGATGGAAATGGACTAGAAACTGGTCCTCAAGCATGGGAAGAGATAGTTGGGTTCACTGAAAAAGTTCAAAAGTCATC
ACCGTACACCTAAGAGCTCCAGCTCTTTTAAACAGTCA

Alignment

ORF - retro_fcat_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.97 %
• Parental protein coverage: 67.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLTLRHINK-VPEHVLRHTQGQRYQRALREYERCQKQGTEYVAACLLHRRRRKEDQVDGAGPPRRGEAFW
          RLTL.HINK.VPEHVLRH.QGQRYQRALREYE.CQKQG.E.V.ACLLH.RR..EDQ.D...PPR..EAFW
Retrocopy RLTLWHINK<VPEHVLRHPQGQRYQRALREYEECQKQGVECVSACLLHKRRPREDQTDSSRPPRLREAFW

Parental  EPSSGEDGAAASDSDDSMTDLYPPEVFTRKDPGGTEHGDGTEDFLTEGEDERPRGLTETGPGGGEETRGD
          EP.S..D.A..SDSDDSMTDL.PPE.FTRKD.GG.EHGD.T.DFLT..ED..P...TE.GPG..EE...D
Retrocopy EPASSNDNATVSDSDDSMTDL*PPELFTRKDLGGNEHGDSTNDFLTKEEDKKP*HPTEKGPGDREEMEMD

Parental  QEPVLKRRKRQLGSAKKFRRHPRKPKSFSNFKQS
          ...VLK..KR.LGS.KKF..H.R.PKS.S.FKQS
Retrocopy *KLVLKHGKR*LGSLKKFKSHHRTPKSSSSFKQS

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	19.40 RPM
SRP017611_kidney	0.00 RPM	58.74 RPM
SRP017611_liver	0.00 RPM	101.49 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_277 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_277 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019763	1 retrocopy	retro_cfam_1702,
Callithrix jacchus	ENSCJAG00000009532	5 retrocopies	retro_cjac_3362, retro_cjac_3452, retro_cjac_3606, retro_cjac_3648, retro_cjac_3914,
Felis catus	ENSFCAG00000028927	1 retrocopy	retro_fcat_277 ,
Monodelphis domestica	ENSMODG00000012766	1 retrocopy	retro_mdom_1894,