RetrogeneDB ID: retro_fcat_1394

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D1:44203540..44204796(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC5
• Ensembl ID: ENSFCAG00000004247
• Aliases: None
• Description: THO complex 5 [Source:HGNC Symbol;Acc:19074]

Sequence

>retro_fcat_1394
ATGTCATCAGAATCAAGCAAGAAACGGAAGCCCAAAGTGATCTGAAGTGATGGAACTCCATCTGAAGGCAAGCGTAACCA
TTCTGACACAGAACAGGAGGGTAAATACTACAGCTAGGAGGCTGAGGTGGACCTGCGGGACCCTGAGAGAGACTATGAGC
TGTACAAGTACACGTGCCAGGAGATGCAGAGGCTCATGGCTGAGATCCAGGACCTGAAGAGCCAAGGAGACAAGGATGTG
GCAGTTGAGATAGAAGATCAGAGGATCCAGAGCTGTGTGCATTTCATGACTCTAAAGAAGCTTAATCGATTGGCCCATAT
CAGGTTGAAGAAAGGAAGAGACCAGACCCATGAGGCCATGCAGAAAGTAGATGCCTATCACCTGCAGCTCCAGAACCTGT
TGTATGAGGTGATGCACCTGCAGAAAGAGATCACCAAATGTCTGGAGTTTAAGTTGAAACATGAAGAAACTGATCTGGTC
AGTTTAGAGGAGTTTTATAAGGAGGCTCCTCCAGATATTAGCAAGGCTGAAGTCACCATGGGAGACCCTCACCAGCAAAC
CCTGGCACATCTGGACTGGGACTGGAGCAGCAAAAAAGGCTGGCAGAGAAGTACCAAGTGTGCCTGTCCAACAAGGAGAA
GATCCTTCAGAAGATTGAGGTGAAGAAGGAATACCTGAGCAGCCTCCATCCTTGCCTCAATAGCATCATGCAGGCTTCCT
TCCCAGTGAAAGAGTACCTATTCATACCGTTCGACCAGGCCCATAAGCAATATGAGACAGCTAGACATCTGCCACCACCT
CTCTATGTCCTCTTTGTCCAGGCCACTGCGTATGGGTAGGCCTGTGATAAGACGTTGTCTGTGGCAATCGAAGGCAGTGT
GGACGAAGCCAAGGCTCTATTTAAGCCTCCTGAAGACTCCCAAGATGATGGGAGTGACTCCGATGCTGAAGAGGAGCAGA
CCACGAAATGCCGGCTACCCACACTGGGAGTTCAGTTGGATGACAAGCGCAAGGAGATGCTGAAGAGGCACCCGCTATCT
GTCATGCTGGACCTGAAGTGCAAAGATGACAGTGTGCTTCACCTGACTTTCTACTACCTCATGAACCTCAACATCATGAC
GGTAAAGGCCAAAGTGACAACCACCACAGAGCTGATCACCCCCATCAGTGCAGGTGACTTGCTGTCTCCTGACTCAGTCC
TGAGCTATTTGTATCCAGGGGATCATGGAAAGAAGACTCCGAATCCAGCCAATCAA

Alignment

ORF - retro_fcat_1394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.38 %
• Parental protein coverage: 61.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSESSKKRKPKVIRSDGAPSEGKRNRSDTEQEGKYYSEEAEVDLRDPGRDYELYKYTCQELQRLMAEIQ
          MSSESSKKRKPKVI.SDG.PSEGKRN.SDTEQEGKYYS.EAEVDLRDP.RDYELYKYTCQE.QRLMAEIQ
Retrocopy MSSESSKKRKPKVI*SDGTPSEGKRNHSDTEQEGKYYS*EAEVDLRDPERDYELYKYTCQEMQRLMAEIQ

Parental  DLKSRGGKDVAVEIEDRRIQSCVHFMTLKKLNRLAHIRLKKGRDQTHEAKQKVDAYHLQLQNLLYEVMHL
          DLKS.G.KDVAVEIED.RIQSCVHFMTLKKLNRLAHIRLKKGRDQTHEA.QKVDAYHLQLQNLLYEVMHL
Retrocopy DLKSQGDKDVAVEIEDQRIQSCVHFMTLKKLNRLAHIRLKKGRDQTHEAMQKVDAYHLQLQNLLYEVMHL

Parental  QKEITKCLEFKSKHEEIDLVSLEEFYEEAPPDISKAEVTMGDPHQQTLARLDWE-LEQRKRLAEKYRECL
          QKEITKCLEFK.KHEE.DLVSLEEFY.EAPPDISKAEVTMGDPHQQTLA.LDW..LEQ.KRLAEKY..CL
Retrocopy QKEITKCLEFKLKHEETDLVSLEEFYKEAPPDISKAEVTMGDPHQQTLAHLDWD<LEQQKRLAEKYQVCL

Parental  SNKEKILKEIEVKKEYLSSLQPRLNSIMQASLPVQEYLFMPFDQAHKQYETARHLPPPLYVLFVQATAYG
          SNKEKIL..IEVKKEYLSSL.P.LNSIMQAS.PV.EYLF.PFDQAHKQYETARHLPPPLYVLFVQATAYG
Retrocopy SNKEKILQKIEVKKEYLSSLHPCLNSIMQASFPVKEYLFIPFDQAHKQYETARHLPPPLYVLFVQATAYG

Parental  QACDKTLSVAIEGSVDEAKALFKPPEDSQDDESDSDAEEEQTTKRRRPTLGVQLDDKRKEMLKRHPLSVM
          .ACDKTLSVAIEGSVDEAKALFKPPEDSQDD.SDSDAEEEQTTK.R.PTLGVQLDDKRKEMLKRHPLSVM
Retrocopy *ACDKTLSVAIEGSVDEAKALFKPPEDSQDDGSDSDAEEEQTTKCRLPTLGVQLDDKRKEMLKRHPLSVM

Parental  LDLKCKDDSVLHLTFYYLMNLNIMTVKAKVTTATELITPISAGDLLSPDSVLSCLYPGDHGKKTPNPANQ
          LDLKCKDDSVLHLTFYYLMNLNIMTVKAKVTT.TELITPISAGDLLSPDSVLS.LYPGDHGKKTPNPANQ
Retrocopy LDLKCKDDSVLHLTFYYLMNLNIMTVKAKVTTTTELITPISAGDLLSPDSVLSYLYPGDHGKKTPNPANQ

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	0.34 RPM	30.41 RPM
SRP017611_kidney	0.62 RPM	23.60 RPM
SRP017611_liver	0.20 RPM	26.49 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1394 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1394 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019894	2 retrocopies	retro_cjac_1965, retro_cjac_2647,
Cavia porcellus	ENSCPOG00000010974	1 retrocopy	retro_cpor_1508,
Felis catus	ENSFCAG00000004247	1 retrocopy	retro_fcat_1394 ,
Myotis lucifugus	ENSMLUG00000012135	1 retrocopy	retro_mluc_2536,
Tursiops truncatus	ENSTTRG00000000542	1 retrocopy	retro_ttru_1315,