RetrogeneDB ID: retro_fcat_1929

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:76080575..76081884(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM184C
• Ensembl ID: ENSFCAG00000015410
• Aliases: None
• Description: transmembrane protein 184C [Source:HGNC Symbol;Acc:25587]

Sequence

>retro_fcat_1929
ATGCCTCGCACTTGTACCAGGAGGAACTGGAGACAGTGAATTTGACCTTTACTGGTGTTTATCTACCTAGTGTACATAGT
GCTTGTGGTTTCTGTATGTGTGTGTGAATTGCAGAAGCTGGAGGTTGGAATACATGCCAAGGCTTGGTTTATTTCTGGAA
TCTTTTTGCTTTTGACTATACCTATACTTGTCTGGGAGATATTGCAACATTTAGTGCATTATACACAACTGAACTACAGA
AACCAATAATAAAGATTCTTTGGATGCCACCCATATACAATTTAGATAGTTGAATAGCTTTGAAATATCACAGCATTGTG
ATATATGTGGATACCTGCAGAGAATGTTATGAAGTTTATGTCATTTACAACTTTATGGGATTCTTTACCAATTATGTAAC
TAACAGGTATCCAAATCTAATATTAACCCTGAAAGCCAAAGATCAGCAGAAACATTCCCTTCATTTATGTTGCTGTCCAC
CATGAACTATAGGAGAAGTATTGCTGTTTCTGTGCAAACTGGGTGTATTGTAGTATACAGTTGTCAGACCATCCACCACC
GTTGTTGCTTTAATCTGTGAGCTGCTTGGTATATATGAAGAGAACTTTAGTTTTTCAAACGCTTTGACTTACTTGGTTAT
AATAAACAACATGCCACAATTGTTTGTCATATATTATCTTCTATTTTATAAAGTACTGAAAGGAAGAAATGAGTTCAATC
CAACCTGTTGGCAAATTTCTTTACGTAAAACTGGTGGTTTTTGTTTCTTTTTGATAAGCAGAAGTTATTGCTTTGCTGGT
AAAATTTGGCATTATTTATGAAAACATATATGGGAATGGCAAACTATAGAAGCTGTGGCTTAAGGACTCCAAGACTTTAT
CATCTGTGTTGATATGTTCTTTGTTTCTATTGCTCATCACTATACTTTCTCACATAAACCATATGTCCAAGAAGCAGAAT
AGGGCTCATGCTTTGATTCCTTTCTTTCCATGTGGGATGTTTCAGATATTAAGGATGATATTTCTGAACAAGTTAAGGCA
TGTTGGAAGGACAGTCACGGGACATCCTTGGAAAAAAGTATTTTCCTGATGATCAAGATCAAAAGGAGCATATAAGCTTG
TCATCCTCATTACCACAAGATGTAATTTCTGTTGCCTTTTTTGTACCACCTTCACCCATGGGTCACTATAAACGGTTTGG
GCATGCTGTGGCTCCCCAGACTATACCTACTATGACTAATATAACTGATGAAACGTGTAATGATACTACAGGAGAGAAAA
AATAACTTTCAGATAAATCCGTGGCCTCC

Alignment

ORF - retro_fcat_1929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 10
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPCTCTWRNWRQWIRPLAVVIYLVSIVVAVPLCVWELQKLEVGIHTKAWFIAGIFLLLTIPISLWVILQH
          MP.TCT.RNWRQ.I.PL.V.IYLV.IV..V..CV.ELQKLEVGIH.KAWFI.GIFLLLTIPI..W.ILQH
Retrocopy MPRTCTRRNWRQ*I*PLLVFIYLVYIVLVVSVCVCELQKLEVGIHAKAWFISGIFLLLTIPILVWEILQH

Parental  LVHYTQ-PELQKPIIRILWMVPIYSLDSWIALKYPSIAIYVDTCRECYEAYVIYNFMGFLTNYLTNRYPN
          LVHYTQ..ELQKPII.ILWM.PIY.LDS.IALKY.SI.IYVDTCRECYE.YVIYNFMGF.TNY.TNRYPN
Retrocopy LVHYTQ<TELQKPIIKILWMPPIYNLDS*IALKYHSIVIYVDTCRECYEVYVIYNFMGFFTNYVTNRYPN

Parental  LVLILEAKDQQKHFPPLCCCPPWTMGEVLLFRCKLGVLQYTVVRPFTTIVALICELLGIYDEGNFSFSNA
          L.L.L.AKDQQKH...LCCCPP.T.GEVLLF.CKLGVL.YTVVRP.TT.VALICELLGIY.E.NFSFSNA
Retrocopy LILTLKAKDQQKHSLHLCCCPP*TIGEVLLFLCKLGVL*YTVVRPSTTVVALICELLGIYEE-NFSFSNA

Parental  WTYLVIINNMSQLFAMYCLLLFYKVL-KEELSPIQPVGKFLCVKLVVFVSFWQAVVIALLVKVGVISE-K
          .TYLVIINNM.QLF..Y..LLFYKVL.KEE.S.IQPVGKFL.VKLVVFVSF..A.VIALLVK.G.I.E.K
Retrocopy LTYLVIINNMPQLFVIY-YLLFYKVL>KEEMSSIQPVGKFLYVKLVVFVSF**AEVIALLVKFGIIYE<K

Parental  HTWEWQTVEAVATGLQDFIICIEMFLAAIAHHYTFSYKPYVQEAEEGSCFDSFLAMWDVSDIRDDISEQV
          H.WEWQT.EAVA.GLQDFIIC..MF...IAHHYTFS.KPYVQEAE.GSCFDSFL.MWDVSDI.DDISEQV
Retrocopy HIWEWQTIEAVA*GLQDFIICVDMFFVSIAHHYTFSHKPYVQEAE*GSCFDSFLSMWDVSDIKDDISEQV

Parental  -RHVGRTVMGHP-RKKFFPEDQDQNEHTSLLSSSSQDAISVASSVPPSPMGHYQGFGHTVTPQTTPTMAN
          .RHVGRTV.GHP..KK.FP.DQDQ.EH.SL.SS..QD.ISVA..VPPSPMGHY..FGH.V.PQT.PTM.N
Retrocopy >RHVGRTVTGHP>GKKYFPDDQDQKEHISLSSSLPQDVISVAFFVPPSPMGHYKRFGHAVAPQTIPTMTN

Parental  IPDEMYNDTTGEKNELSDKSVAS
          I.DE..NDTTGEK..LSDKSVAS
Retrocopy ITDETCNDTTGEKK*LSDKSVAS

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	33.86 RPM
SRP017611_kidney	0.00 RPM	67.92 RPM
SRP017611_liver	0.00 RPM	25.98 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1929 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1929 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002418	1 retrocopy	retro_cjac_2276,
Felis catus	ENSFCAG00000015410	2 retrocopies	retro_fcat_1929 , retro_fcat_755,
Homo sapiens	ENSG00000164168	1 retrocopy	retro_hsap_4870,
Macaca mulatta	ENSMMUG00000004977	1 retrocopy	retro_mmul_2611,
Otolemur garnettii	ENSOGAG00000015819	1 retrocopy	retro_ogar_3118,
Tarsius syrichta	ENSTSYG00000005633	1 retrocopy	retro_tsyr_1001,