RetrogeneDB ID: retro_fcat_1577

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:30489429..30490113(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000022306
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSN
• Ensembl ID: ENSFCAG00000027149
• Aliases: None
• Description: translin [Source:HGNC Symbol;Acc:12379]

Sequence

>retro_fcat_1577
ATGTCTGTGAGTGAGATCTTCGTGGAGCTGCAGGGCTTTTTGGCTGCCAAGCAGGACATCTAAGAGGAAATCTGAAAAGT
TGTACAAAGTTTATAACAAACAGCTTAAGCGATTTTAACTCTACTGCAAGGGGTCCAGCAGGGTCCTGGTTTTCAGGATA
TTCCAAAGAGGTGTTTGAAAGCTTGAGAACACTTTGGTACAGTAAAAACACATTTAATGTCTTCAGAGACCAAGTTCTCT
GCTGAACAGTATTACGGATTTCATGAGCACTGGGGGTTTGTGCTGCAGCTTTTGGTCTTCTTGGTAACATTTGTTGTGTA
TTTGGAATCAGAAACACTAATGACTCCAGAAGTGGTTACTGAAGTTCTTGGCATTGAGCCATATTGGGAGAAAGGATTTC
ATCTGGATGTAGAAGATCATCTTTCAGGAGTTCTAATTCTTGCCAGTGAATTTTCAAGGCTCTCTGTCAACAGTGTGACT
GTTGGAGGCTACTCCCAGATCCTCCACATCTACACTTTCATTAATGAACTGAATTCTAGCTTCTGCCTTCCCAACCCGAA
AAACGACTCCCTGAGGAATTGCTGTGATGGCTTCAAGTATGATCTGAAAAAAGTAGAGGAGGTGGTCTGTGATCTCACCA
TCCAGGGCTTCAGTAAGGAGACAGCAGTGGCTTATGCAGAGAAA

Alignment

ORF - retro_fcat_1577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKT
          MSVSEIFVELQGFLAA.QDI.EEI.KVVQSL.QTA..ILTLLQGV.QG.GFQDIPKRCLKA.EHFGTVKT
Retrocopy MSVSEIFVELQGFLAAKQDI*EEI*KVVQSL*QTA*AILTLLQGVQQGPGFQDIPKRCLKA*EHFGTVKT

Parental  HLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLESETLVTREAVTEILGIEPDREKGFHLDVEDY
          HL.S..TKF.AEQYY.FHEHW.FVLQ.LVFL..FVVYLESETL.T.E.VTE.LGIEP..EKGFHLDVED.
Retrocopy HLMSSETKFSAEQYYGFHEHWGFVLQLLVFLVTFVVYLESETLMTPEVVTEVLGIEPYWEKGFHLDVEDH

Parental  LSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKVEEVVY
          LSGVLILASE.SRLSVNSVT.G.YS..LHI.TFINEL.S.F.L.N.KNDSLR...DG.KYD.KKVEEVV.
Retrocopy LSGVLILASEFSRLSVNSVTVGGYSQILHIYTFINELNSSFCLPNPKNDSLRNCCDGFKYDLKKVEEVVC

Parental  DLSIRGFNKETAAACAEK
          DL.I.GF.KETA.A.AEK
Retrocopy DLTIQGFSKETAVAYAEK

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	16.99 RPM
SRP017611_kidney	0.00 RPM	14.02 RPM
SRP017611_liver	0.00 RPM	7.48 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1577 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1577 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006059	1 retrocopy	retro_btau_1598,
Dasypus novemcinctus	ENSDNOG00000025740	2 retrocopies	retro_dnov_1581, retro_dnov_907,
Felis catus	ENSFCAG00000027149	1 retrocopy	retro_fcat_1577 ,
Homo sapiens	ENSG00000211460	1 retrocopy	retro_hsap_3760,
Gorilla gorilla	ENSGGOG00000002216	2 retrocopies	retro_ggor_2528, retro_ggor_2610,
Myotis lucifugus	ENSMLUG00000012656	1 retrocopy	retro_mluc_1420,
Macaca mulatta	ENSMMUG00000021119	1 retrocopy	retro_mmul_1718,
Monodelphis domestica	ENSMODG00000000147	1 retrocopy	retro_mdom_1896,
Nomascus leucogenys	ENSNLEG00000001202	1 retrocopy	retro_nleu_170,
Ornithorhynchus anatinus	ENSOANG00000003457	1 retrocopy	retro_oana_120,
Oryctolagus cuniculus	ENSOCUG00000023529	1 retrocopy	retro_ocun_271,
Otolemur garnettii	ENSOGAG00000030436	3 retrocopies	retro_ogar_1221, retro_ogar_2875, retro_ogar_3426,
Pan troglodytes	ENSPTRG00000012420	1 retrocopy	retro_ptro_2551,
Tarsius syrichta	ENSTSYG00000004395	1 retrocopy	retro_tsyr_1593,