RetrogeneDB ID: retro_fcat_1942

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:104907252..104907773(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000004274
• Aliases: None
• Description: None

Sequence

>retro_fcat_1942
CCCATCCAGGCCCAAGACTCAGATCCCCACTCTTCTACCCTTGGCTTTTCATGGACACCTATGAAGACCAGCGGTGGAGA
GCTCTCAAGCCCACTGGTCAAACAGCTGAGTGAAGTATTTGAGAACAAAGCCCCCAAATCAAATCTTCCCCCAGAGTCTG
TTCTGCCTCTAGAGTCAACTTCATCTTCTGAATTGGACTTACCTCTGGGCACCTAGTTTTCCCTTGAGGACCAGATGCCA
CCTTGGAGCCAGATTGGGCTCCCCTACAAGCAAGTGTTCTCTAAGGAAGAAGCATGACAGCCCTCAGAAACCCCCATGGT
AGGCCAAGTGTCAACAAATCCTTGAGAGTTCCTGAGACTTGCTGATCTTCAGGATCTAAGCATGATAGATGGAAAGCAAA
TGGCAAGATACTAGGGAGATCCACCCTCACCATCCTAGAGGATTAGAACTCCGCTGGAACTCTGACACTACAACAGGGTA
AATGGCTTCCACCCCTACCCCCCCAAATGAAAATACTACGG

Alignment

ORF - retro_fcat_1942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 64.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PNEAQDSDPRSPTLGIARTPMKTSSGEPPSPLAKQLNEVFEKEASKLNRPPELVLPLEATSPSELNLPLG
          P..AQDSDP.S.TLG...TPMKTS.GE..SPL.KQL.EVFE..A.K.N.PPE.VLPLE.TS.SEL.LPLG
Retrocopy PIQAQDSDPHSSTLGFSWTPMKTSGGELSSPLVKQLSEVFENKAPKSNLPPESVLPLESTSSSELDLPLG

Parental  TQFSLEDRMPLWSQTELPSKQVSSKEEAGQPSQPPTASQGSDKP-LRDPETPRSSGSKHNRRKGNGKVLG
          T.FSLED.MP.WSQ..LP.KQV.SKEEA.QPS..P...Q.S..P.LR.PET..SSGSKH.R.K.NGK.LG
Retrocopy T*FSLEDQMPPWSQIGLPYKQVFSKEEA*QPSETPMVGQVSTNP<LRVPETC*SSGSKHDRWKANGKILG

Parental  RSPLTILQDDNSPGTLTPRQGKRPPPLSENARALK
          RS.LTIL.D.NS.GTLT..QGK..PPL......L.
Retrocopy RSTLTILED*NSAGTLTLQQGKWLPPLPPQMKILR

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	0.23 RPM
SRP017611_kidney	0.00 RPM	0.82 RPM
SRP017611_liver	0.00 RPM	1.01 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1942 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1942 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013985	1 retrocopy	retro_amel_1158,
Canis familiaris	ENSCAFG00000014650	4 retrocopies	retro_cfam_1100, retro_cfam_1940, retro_cfam_345, retro_cfam_633,
Cavia porcellus	ENSCPOG00000012334	1 retrocopy	retro_cpor_1073,
Felis catus	ENSFCAG00000004274	2 retrocopies	retro_fcat_1182, retro_fcat_1942 ,
Mustela putorius furo	ENSMPUG00000016781	1 retrocopy	retro_mputfur_663,
Pteropus vampyrus	ENSPVAG00000012300	4 retrocopies	retro_pvam_235, retro_pvam_248, retro_pvam_297, retro_pvam_667,
Rattus norvegicus	ENSRNOG00000015529	1 retrocopy	retro_rnor_2685,
Ictidomys tridecemlineatus	ENSSTOG00000023573	1 retrocopy	retro_itri_804,
Tupaia belangeri	ENSTBEG00000001905	1 retrocopy	retro_tbel_534,
Vicugna pacos	ENSVPAG00000009784	1 retrocopy	retro_vpac_296,