RetrogeneDB ID: retro_fcat_1284

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:91006888..91007604(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATF1
• Ensembl ID: ENSFCAG00000013892
• Aliases: None
• Description: activating transcription factor 1 [Source:HGNC Symbol;Acc:783]

Sequence

>retro_fcat_1284
GTATCATCTTTATCAGAAAGTGAGGAGTCTCAGGACTCATCAGACGGTATAGGCTCTTCACAGAAAGCCTGCGGGATCCT
AGCATGGTGTGCATCTAGCAGAAAAATTTTGAAAGGTTTATCTTCTGAAGATACATGGGGCAGAACAGAAGACAGAGAAA
ACCCTGGAGTTTCTGCTGTCACTTCTATGTCTGTCCCAACTCCCATCTATCAAACTAGCAATGGACAGTACATTGCCATT
GCCCCAAAGGGAGACTTACAACTGGCCAGTTCAGGCACAGATGGAGTATAGGGACTTCAGACATTAACCATGACAAATTC
AGTCAGTACTCAGCAAGGGACAACAATTCTCCAGCATGCACAGACCTCCGATGGACAGCAAATACTTGTGCCTAGCAACC
AGGTGGTTGTACAAACTGCATCAGGAGATATGCACACATATCAGATCTGTACCACCCCTTCAGCTATTTCGCTGCCACAA
CCTGTGGTAATGATATTTCCTGTGACACTTATATCTCAGACAACTAAGACAGATGACCCCCAACTGAAAAGAGAAATAGG
TCAATGAAAAACAGAGAAGCTGCGCAAGAATGTCTCAGAAAGAAGAAAGAATATGTGAAATGCCTGAATAATCAGGTTGC
AGTCTTGGAAAATCAAAATAAAACTCTAATAGAAGAGTTAAAAACTTTGAAGGATCTTTATTCCCATAAAGATATT

Alignment

ORF - retro_fcat_1284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.12 %
• Parental protein coverage: 86.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSSLSESEESQDSSDSIGSSQKAHGILARRPSYRKILKDLSSEDTRGRKGDGENPGVSAVTSMSVPTPIY
          VSSLSESEESQDSSD.IGSSQKA.GILA...S.RKILK.LSSEDT.GR..D.ENPGVSAVTSMSVPTPIY
Retrocopy VSSLSESEESQDSSDGIGSSQKACGILAWCASSRKILKGLSSEDTWGRTEDRENPGVSAVTSMSVPTPIY

Parental  QTSSGQYIKVAIAPNGALQLASPGTDGVQGLQTLTMTNSGSTQQGTTILQYAQTSDGQQILVPSNQVVVQ
          QTS.GQYI..AIAP.G.LQLAS.GTDGV.GLQTLTMTNS.STQQGTTILQ.AQTSDGQQILVPSNQVVVQ
Retrocopy QTSNGQYI--AIAPKGDLQLASSGTDGV*GLQTLTMTNSVSTQQGTTILQHAQTSDGQQILVPSNQVVVQ

Parental  TASGDMQTYQIRTTPSATSLPQTVVMTSPVTLTSQTSKTDDPQLKREI-RLMKNREAARECRRKKKEYVK
          TASGDM.TYQI.TTPSA.SLPQ.VVM..PVTL.SQT.KTDDPQLKREI.R.MKNREAA.EC.RKKKEYVK
Retrocopy TASGDMHTYQICTTPSAISLPQPVVMIFPVTLISQTTKTDDPQLKREI<RSMKNREAAQECLRKKKEYVK

Parental  CLENRVAVLENQNKTLIEELKTLKDLYSHKSV
          CL.N.VAVLENQNKTLIEELKTLKDLYSHK..
Retrocopy CLNNQVAVLENQNKTLIEELKTLKDLYSHKDI

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	2.98 RPM
SRP017611_kidney	0.00 RPM	7.21 RPM
SRP017611_liver	0.00 RPM	6.67 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1284 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1284 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004733	5 retrocopies	retro_chof_1987, retro_chof_2305, retro_chof_27, retro_chof_462, retro_chof_760,
Felis catus	ENSFCAG00000013892	1 retrocopy	retro_fcat_1284 ,
Microcebus murinus	ENSMICG00000003301	1 retrocopy	retro_mmur_1336,
Sarcophilus harrisii	ENSSHAG00000004637	2 retrocopies	retro_shar_221, retro_shar_635,