RetrogeneDB ID: retro_fcat_172

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:124354600..124355812(+)
• Located in intron of: ENSFCAG00000010575

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX5
• Ensembl ID: ENSFCAG00000003512
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 5 [Source:HGNC Symbol;Acc:2746]

Sequence

>retro_fcat_172
AGGTTTGAGGGAAGTAGGGCAGGGCATCTATCTGGAAAGAAGTTTAGAAATTCTGGGGGAAAACTAGTCAAAAAAAGAAG
TGGGATCTTGATGAGCCGCCCAAATTTGAGACAAATTTTTAGTGAGGTTTGGCGAGGCACACTGTACAAGAGGTGGAAAC
ATATAGAAGGCATAAGGAAATTACACATTGCAGTTAGAGGTCACAAGTGCCCAAAGTCCGTTCTGAATTTTTATGAGGCA
AACTTGCCTGCAAATGTAATGGTTGTCATTGTAAGATCAAATTTTATTGAACATGCTGCTGTTACAAGGTCAGTGATAGC
TCCTAACTCCAAGTGGATTGGATATGGTTGGAGCAGCACAGACTGGATCCAGGAAAACATTGTCTTATTTGCTGTCTGCT
CTCCTCCACATCCATCAGCCATTCCTAAAGAGAGGTGATGGGTGTGTTTGCTTGGTGCTGGCACCAACTTGAGAACTGGC
CTAACATGTACAGCAAGTAGCTGCTGAATACTGTAGAGCATGTCAGTGGAAGTCCACTTGCATCTATGGTGGTGCTCCTC
AGGGACCACATATTTGTGATTTGGAGAGAGGTGTGGAAATCTGTATTGCATTACCTGGAAGACTTTATTTAGAGTGTGGA
AAACCAGTCAGAGAAGAACCACCTATCTTGTCCTTGATGAAGTAGATGGAATGCTTATAGGGGCTTCAAGCCCCAAATAA
GGAAGATTGTGGATCAGATAGGACCTGACAGGCAAACCCTAATGTGGAGTGTGACTTGGCCCAAAGAAGTAAGACAGCAT
GTTAAAGATTCTCTTAAAGAACTACATTCGTATAAACGTTAGTGCAGTAGAACTGACTGCAAACCACAACATTCTTCACA
TTGTAGGTGTGTGTCATGATGCAGAAAAGGATGAAAAACTTACTCGTCTAATAGAAGAGATCATGAGAAAGGAGTACAAT
AAGACCATTTTTGTTGTTGTTGAAACCAAAAAAAGATGTGATGAGCTTACTAGATAAATGAGAGATGGGTGTCCCACCAT
GGGTATCCATAGTGACAAGGGTCAACAGGAATATGACTGGGTTCTAAATGAATTCAGACATGGAAAAGCTCCTATTCTGG
TTGCTACAGATGTCACCTCCAGAGGACTAGATGTGGAAGATGTGAAATTTGTCATTGGATATTACCCTAACTCCTCAAGG
AGTTCATTAAAT

Alignment

ORF - retro_fcat_172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.6 %
• Parental protein coverage: 59.91 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RFGGSRAGPLSGKKFGNPGEKLV-KKKWNLDELPKFEKNFYQEHPDLARRTAQEVETYRRSKEITVRGHN
          RF.GSRAG.LSGKKF.N.G.KLV.K....L...P.....F...............E..R....I.VRGH.
Retrocopy RFEGSRAGHLSGKKFRNSGGKLVKKRSGILMSRPNLRQIFSEVWRGTLYKRWKHIEGIRKL-HIAVRGHK

Parental  CPKPVLNFYEANFPANVMDVIARQNFTEPTAI-QAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHIN
          CPK.VLNFYEAN.PANVM.VI.R.NF.E..A..Q.Q......SGLDMVG.AQTGS.KTLSYLL.A..HI.
Retrocopy CPKSVLNFYEANLPANVMVVIVRSNFIEHAAV>QGQ**LLTPSGLDMVGAAQTGSRKTLSYLLSALLHI-

Parental  HQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGR
          HQPFL.RGDG..CLVLAPT.ELA..VQQVAAEYCRAC..KSTCIYGGAP.GP.I.DLERGVEICIA.PGR
Retrocopy HQPFLKRGDGCVCLVLAPT*ELA*HVQQVAAEYCRACQWKSTCIYGGAPQGPHICDLERGVEICIALPGR

Parental  LIDFLECGK-TNLRRTTYLVLDEADRMLD-MGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAED-FL
          L...LECGK.T..RRTTYLVLDE.D.ML...GF.PQIRKIVDQI.PDRQTLMWS.TWPKEVRQ...D..L
Retrocopy L--YLECGK<TSQRRTTYLVLDEVDGMLI<RGFKPQIRKIVDQIGPDRQTLMWSVTWPKEVRQHVKD>LL

Parental  KDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTI-VFVETKRRCDELTRKMRR
          K.YI.IN..A.EL.ANHNIL.IV.VCHD.EKDEKL.RL.EEIM....NKTI.V.VETK.RCDELTR.MR.
Retrocopy KNYIRINVSAVELTANHNILHIVGVCHDAEKDEKLTRLIEEIMRKEYNKTIFVVVETKKRCDELTR*MR-

Parental  DGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYIH
          DG.P.MGIH.DK.QQE.DWVLNEF.HGKAPIL.ATDV.SRGLDVEDVKFVI.Y.YPNSS.....
Retrocopy DGCPTMGIHSDKGQQEYDWVLNEFRHGKAPILVATDVTSRGLDVEDVKFVIGY-YPNSSRSSLN

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	503.05 RPM
SRP017611_kidney	0.10 RPM	488.91 RPM
SRP017611_liver	0.00 RPM	371.10 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_172 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_172 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019950	1 retrocopy	retro_etel_1009,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172 ,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583,
Myotis lucifugus	ENSMLUG00000009496	4 retrocopies	retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788,
Pteropus vampyrus	ENSPVAG00000001932	1 retrocopy	retro_pvam_1267,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260,
Tarsius syrichta	ENSTSYG00000012149	1 retrocopy	retro_tsyr_1269,
Tursiops truncatus	ENSTTRG00000008793	1 retrocopy	retro_ttru_1662,