RetrogeneDB ID: retro_fcat_634

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:90533322..90533696(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX8
• Ensembl ID: ENSFCAG00000008276
• Aliases: None
• Description: syntaxin 8 [Source:HGNC Symbol;Acc:11443]

Sequence

>retro_fcat_634
AGATACACTCTGATGACTGAAGAAGCTAAGGGAGAAGTACCCAACCTTTGACTCCTTGAGGAGCCAAGGAAAACTAGAGG
CTTGGGTTTTGATGAAATCCTCCAACGGCACCAGAAAATTATCTAAGAACAGGATGCAGGCCTTGAGGTCTTTTCCTTTA
TCAAAAATCACCATAAACAAATGGGGCAGGAAATTGTTAATGTGCTGGATGAACAAAACAAGATAATTGATGAATTTGCT
GACCTGGTGAAGAAGACACATGAAAAGCTTTAAACTGAAACCAGGGATGTGAATATGGTGGATAGAAATTTAGCATCTTG
TGAGTTTATAATGGTGATTTCATTGCTGTTATGGCGGTTGTTGCAGTCTGGCCA

Alignment

ORF - retro_fcat_634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.94 %
• Parental protein coverage: 55.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSSLMTGGAKRGVPNPWLFEEPEETRGLGFDEIRQQQQKIIQEQDAGLDALSSIISRQKQMGKEIGNELD
          R..LMT..AK..VPN..L.EEP..TRGLGFDEI.Q..QKII.EQDAGL...S.I....KQMG.EI.N.LD
Retrocopy RYTLMTEEAKGEVPNL*LLEEPRKTRGLGFDEILQRHQKII*EQDAGLEVFSFIKNHHKQMGQEIVNVLD

Parental  EQNEIIDDLANLVENTDGKLRTETRRMNIVDRKSTSCGMVMVILLLL-VAIVVVAVWP
          EQN.IID..A.LV..T..KL.TETR..N.VDR...SC...MVI.LLL..A.V..AVWP
Retrocopy EQNKIIDEFADLVKKTHEKL*TETRDVNMVDRNLASCEFIMVISLLL<MAVV--AVWP

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	15.04 RPM
SRP017611_kidney	0.00 RPM	25.46 RPM
SRP017611_liver	0.00 RPM	10.51 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_634 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_634 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002045	1 retrocopy	retro_amel_911,
Canis familiaris	ENSCAFG00000017413	1 retrocopy	retro_cfam_1959,
Cavia porcellus	ENSCPOG00000002114	1 retrocopy	retro_cpor_1034,
Felis catus	ENSFCAG00000008276	1 retrocopy	retro_fcat_634 ,
Myotis lucifugus	ENSMLUG00000008612	1 retrocopy	retro_mluc_2329,
Mustela putorius furo	ENSMPUG00000007815	2 retrocopies	retro_mputfur_975, retro_mputfur_996,
Pteropus vampyrus	ENSPVAG00000001001	1 retrocopy	retro_pvam_147,
Rattus norvegicus	ENSRNOG00000003849	2 retrocopies	retro_rnor_2422, retro_rnor_2500,
Tarsius syrichta	ENSTSYG00000010795	1 retrocopy	retro_tsyr_1906,