RetrogeneDB ID: retro_fcat_1839

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:23261779..23262733(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000015735
• Aliases: None
• Description: None

Sequence

>retro_fcat_1839
CACATGGCAATTCTTAAGGAAAAACTGATGGCACCAGTTGCAGAAGAAGAGACAACTGTCCCAAACAATAAGATCACTGC
AATAGGTGTTGAACAAGTTGGTATGGCATGTGCCATCAGCATTCTGGGAAAGTCTCTGGCTCATGACCTTGCCCTTCTGT
ATGTTTTAGAAGATAAAGTCAGAGGAGAAATGATGGATCTGCAACATGGGAGCTGATTTCTTCAGACACCAAAAAATTGT
GGCAGATAAAGATTACTCTGTGACTACCAATTCTAAGATTGTGGTGGTAACAGCAGGAGTCCACCAGCAGGAGGGAGAGA
GCCATCTCAATCTGGTGAAGAGGAATGTTAATGTCTTCAAATTCATTATTCCTCAGATAGTCAATCACAGGCCTGATTGT
ATCATAACCATGGTTTACAACTCAGTGGATATTCTCACATAGGTTACCTGGAAACTTAAGTGGACTACCCAAACACCATG
TGATTGGAAGTAGGTATAACATGGATTCCACTAGATTTTGCTGCCTTATGGCTGAAAAACAAGGCATTCGTCCCAGCAGC
TGCCATGGATGGATCTGGGAGAACATGGCGACTCAGGCGTGGCTGTGTGGAATGGAGTGAATGTGGTGTTTCTCTCCAAG
AACTGAATCCAGAAATGGGAACAGACAATGACAGTGAAAATTGGAAGTAAGTGCATAAGATGATGGTTGAAAGTGCCTAT
GAAGCCACTAAGCTAAAAGGATATACCAACTGGGCTATTGGATTAAGTGTGGCTGATCTCATTGAATCCATATTGGAAAA
TCTATCCAGGATTCATCCAGTGTCAAGAATGGTGAAGTGGATGTATGGCATTGAGAATGAAGTCTTCCTGAGCCTTCTGT
GTATCCTGAATGATCGGGGATTAACCAGTATTATGATCCGGAAGCTGAAGAATGATGAAGTCACTCAGCCCAAA

Alignment

ORF - retro_fcat_1839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.75 %
• Parental protein coverage: 88.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NMATLKDQLIQNLLKEDHT-PQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHG
          .MA.LK..L......E..T.P.NKIT..GV..VGMACAISIL.K.LA..LAL..V.EDK..GEMMDLQHG
Retrocopy HMAILKEKLMAPVAEEETTVPNNKITAIGVEQVGMACAISILGKSLAHDLALLYVLEDKVRGEMMDLQHG

Parental  SLFLRTPK-IVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLVVS
          S.FL.TPK.IV..KDY.VT.NSK.V..TAG..QQEGES.LNLV.RNVN.FKFIIP..V...P.C....V.
Retrocopy S*FLQTPK>IVADKDYSVTTNSKIVVVTAGVHQQEGESHLNLVKRNVNVFKFIIPQIVNHRPDCIITMVY

Parental  NPVDILTYVAWK-ISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWV-LGEHGDSSVPVWSGVN
          N.VDILT.V.WK..SG.PK..VIGS..N.DS.RF..LM.E..G....SCHGW..LGEHGDS.V.VW.GVN
Retrocopy NSVDILT*VTWK>LSGLPKHHVIGSRYNMDSTRFCCLMAEKQGIRPSSCHGWI<LGEHGDSGVAVWNGVN

Parental  VAGVSLKN-LHPDLGTDADKEKWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPIS
          V...S.KN.L.P..GTD.D.E.WK.VHK..V.SAYE..KLKGYT.WAIGLSVADL.ESI..NL.R.HP.S
Retrocopy VVFLS-KN<LNPEMGTDNDSENWK*VHKMMVESAYEATKLKGYTNWAIGLSVADLIESILENLSRIHPVS

Parental  TMIKGLYGIKDDVFLSVPCILGQNGISDVVKVTLTPEEEARLK
          .M.K..YGI...VFLS..CIL...G........L...E....K
Retrocopy RMVKWMYGIENEVFLSLLCILNDRGLTSIMIRKLKNDEVTQPK

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	0.11 RPM	109.03 RPM
SRP017611_kidney	0.62 RPM	163.24 RPM
SRP017611_liver	0.00 RPM	655.67 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1839 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1839 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 7 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009211	8 retrocopies	retro_cfam_1061, retro_cfam_1149, retro_cfam_1182, retro_cfam_1317, retro_cfam_1617, retro_cfam_1946, retro_cfam_2006, retro_cfam_309,
Dipodomys ordii	ENSDORG00000003524	2 retrocopies	retro_dord_439, retro_dord_449,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Felis catus	ENSFCAG00000015735	4 retrocopies	retro_fcat_102, retro_fcat_1839 , retro_fcat_1919, retro_fcat_295,
Myotis lucifugus	ENSMLUG00000016343	4 retrocopies	retro_mluc_1716, retro_mluc_2031, retro_mluc_2440, retro_mluc_365,
Ictidomys tridecemlineatus	ENSSTOG00000000014	3 retrocopies	retro_itri_1396, retro_itri_1526, retro_itri_535,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,