RetrogeneDB ID: retro_fcat_1157

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:213344863..213345526(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMAP1
• Ensembl ID: ENSFCAG00000007247
• Aliases: None
• Description: small ArfGAP 1 [Source:HGNC Symbol;Acc:19651]

Sequence

>retro_fcat_1157
ATGACTTCGAATCCCTTACCTCCAACCGTCTACGCCCCCAGCTCCGGGGACGTCCTCTATACCTGCAGCTGCCACTCTGT
CTACGTTAATATCTGGGGTGCTCGATCTGTTCACTCAGCAAGCTACAAAGTCAGAAGAGGTGGGGAAGAAGCAACGCTCC
AAAGGTTCCATCTTCTCTCTGTGTGGTACAGGAACCGTTCGGCAGAAGAGTACTCCTGGTGTGCTTATGGGACGCACAAT
TATGCCCTTTGCCTCACGAGCACCGTCTGTCTTTCAAGGCTTTCCATCGATGGGCACGCCTGTGCCTCCACCTGCAGCTC
CTGGTCTTCTAGGAAATGTGATGGGACAGAGCGCCAGTCTGATGGTGGGCATGCCCAGGCCCAGCAGGTCTATGGGAAAC
ACATGAACCGGTGTGATGTCACTTCCTTCAAATGTGGTCGGCCCCCAAGGAGGAACCGTAGGACAGAGGGGCGCACCCTC
GGGTGAGCTTGGCCTGCCGCAAGCTCAACGGCCCCAGCAGAACCTCTCGCAGATGAATCAGCAAATGGCTGGCACGGGTA
TCAGTAGTACGAACCCTGCAATGGGTTTTGGCCAGCCCCCAACACAACAGCAGTTTGGCCCGGAAGCTCATCCGTTCAGA
CTCTCGGCACACAGCTGTGGAAA

Alignment

ORF - retro_fcat_1157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MISNPLPATVI-PTAQGTPSIPAAATLSTVISGDLDLFTEQATKSEEVAKKQLSKDSILSLYGTGTIQQQ
          M.SNPLP.TV..P.A.GT.SIPAAATLST.ISG.LDLFT.QATKSEEV.KKQ.SK.SI.SL.GTGT..Q.
Retrocopy MTSNPLPPTVY>PPAPGTSSIPAAATLSTLISGVLDLFTQQATKSEEVGKKQRSKGSIFSLCGTGTVRQK

Parental  STPGVFMGPTNIPFTSQAPTAFQGFPPMGVPVPAPAAPGLLGNVMGQSTSMMVGMPMPNGFMGNAQTGVM
          STPGV.MG.T..PF.S.AP..FQGFP.MG.PVP.PAAPGLLGNVMGQS.S.MVGMP.P...MGN..TGVM
Retrocopy STPGVLMGRTIMPFASRAPSVFQGFPSMGTPVPPPAAPGLLGNVMGQSASLMVGMPRPSRSMGNT*TGVM

Parental  PLPPNVVGPHGGMVGQMGAPQSKFGLPQAQQPQWNLSQMNQQMAGMSISSTNPAVGFGQP-PSTTAGWSG
          .LP.NVVGP.GG.VGQ.GAP....GLPQAQ.PQ.NLSQMNQQMAG..ISSTNPA.GFGQP.P.TTA.W.G
Retrocopy SLPSNVVGPQGGTVGQRGAPSGELGLPQAQRPQQNLSQMNQQMAGTGISSTNPAMGFGQP<PNTTAVWPG

Parental  SSSGQTLSTQLWK
          SSS.QTL.TQLWK
Retrocopy SSSVQTLGTQLWK

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	31.91 RPM
SRP017611_kidney	0.00 RPM	11.23 RPM
SRP017611_liver	0.00 RPM	6.77 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1157 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1157 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
Echinops telfairi	ENSETEG00000001865	1 retrocopy	retro_etel_1525,
Felis catus	ENSFCAG00000007247	1 retrocopy	retro_fcat_1157 ,
Loxodonta africana	ENSLAFG00000007948	1 retrocopy	retro_lafr_530,
Mus musculus	ENSMUSG00000026155	1 retrocopy	retro_mmus_3253,