RetrogeneDB ID: retro_fcat_467

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:49004191..49004986(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEA3
• Ensembl ID: ENSFCAG00000011648
• Aliases: None
• Description: transcription elongation factor A (SII), 3 [Source:HGNC Symbol;Acc:11615]

Sequence

>retro_fcat_467
CTATTGAACTCCCCTGGACCTCCCAAAGAAGAAAAAGGAGAAGAAAGAGACAAAGCAAAGAAAGAAAAAGGACTTGACTG
TTCTCATCAGAAACCAGAGGCAGGACTTTTTCCACCAAGGAAAAAAACAAGGACAAGAGCCCAAAGACAGGAGAGACTCT
GTGGACTCCAAGTCTTCAGCCAACTCCTTTACAAAAAGGCCATCGATGGAAAGATCAAACAGCAGCAAATCAAAAGCAGA
GACTCCAAAAACACCCAGCAGCACCTCAATCCTTACTTTTGCCCCCTCCATCTATCTCCTGGCACCCTACTATCCCATAG
GGTACTCTGTGCAGGATAAGTGTGTGGAAATGCCCTCAGCAGCCCTGAAGGCTGATGACAATTGCAAGGACTATGGAGCC
AACTGTGACAAGAAGTCATCAGAAATTGAAGATCATATCTATTAGGAGCTCAAGAGCACTGACATGAAGTACTGGAACCA
AGTTCACAGACAAATAAGCAAACTTGTGGACTCCAGGAATCCATTCTGAGGAATAATGTTCTCAGTGGGGCCATCTCTGT
TGTGCTTATTGCCAGGAAGATGACAGAGGAAATGGCCAGTGATGAGCTGAGAGAATTGAGAAATTCCATGACCCAGAAGG
TTACCTGTGAGCATCAGATGGCCAAGATGGGTGGCACCACCACTGACCTCTTCCAGTGCAGTAGATGGAAGAACTGTACC
CAAAACTAGGTGCAGACATGCAGTGCTGAGCCCATGAATACCTTTGTCTTATGTAATGAATACGGCAGTCACTGG

Alignment

ORF - retro_fcat_467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.52 %
• Parental protein coverage: 76.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLDSPGPPKGEKREERDKAKKEKGLNCSDWKPEAGL-SPPRKKR-EDPKDRRDSVDSKSSATSSPKRPSM
          LL.SPGPP................L.CS..KPEAGL..P..K.R...PKDRRDSVDSKSSA.S..KRPSM
Retrocopy LLNSPGPPXXXXXXXXXXXXXXXXLDCSHQKPEAGLFPPRKKTR>QEPKDRRDSVDSKSSANSFTKRPSM

Parental  ERSNSSKSKAETPKTPTSPSTPTFAPSICLLAPCYLTGDSVRDKCVEMLSAALKAEDDYKDYGVNCDKMA
          ERSNSSKSKAETPKTP.S.S..TFAPSI.LLAP.Y..G.SV.DKCVEM.SAALKA.D..KDYG.NCDK..
Retrocopy ERSNSSKSKAETPKTPSSTSILTFAPSIYLLAPYYPIGYSVQDKCVEMPSAALKADDNCKDYGANCDKKS

Parental  SEIEDHILEELKSTDMKYRNRVRSRISNLKDPRNP-SLRRNVLSGAISAGLIAKMTAEEMASDELRELRN
          SEIEDHI..ELKSTDMKY.N.V...IS.L.D.RNP..LR.NVLSGAIS..LIA....EEMASDELRELRN
Retrocopy SEIEDHIY*ELKSTDMKYWNQVHRQISKLVDSRNP<ILRNNVLSGAISVVLIARKMTEEMASDELRELRN

Parental  AMTQEAIREHQMAKTGGTTTDLFQCSKCKKKNCTYNQVQTRSADEPMTTFVLCNECGNRW
          .MTQ....EHQMAK.GGTTTDLFQCS....KNCT.N.VQT.SA.EPM.TFVLCNE.G..W
Retrocopy SMTQKVTCEHQMAKMGGTTTDLFQCSRW--KNCTQN*VQTCSA-EPMNTFVLCNEYGSHW

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	0.92 RPM
SRP017611_kidney	0.00 RPM	92.24 RPM
SRP017611_liver	0.00 RPM	39.02 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_467 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_467 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009579	1 retrocopy	retro_amel_1875,
Felis catus	ENSFCAG00000011648	1 retrocopy	retro_fcat_467 ,