RetrogeneDB ID: retro_fcat_1175

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:40745062..40745951(-)
• Located in intron of: ENSFCAG00000022018

Retrocopy information

• Ensembl ID: ENSFCAG00000031410
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AMD1
• Ensembl ID: ENSFCAG00000028033
• Aliases: None
• Description: adenosylmethionine decarboxylase 1 [Source:HGNC Symbol;Acc:457]

Sequence

>retro_fcat_1175
AGATCCGAGTGGGACATACTTTTTGAAGGATGTGCAATGTTCAATCATAAGTGTGACAACTGACAAGCAGGAAGCTTATG
TACTCAGTGAGAGTAGCACGTTTGTCTCTAAGAGACGTTTCATTTTGAAGACCTCTGGTACCACCCTCTTGCTGAAAATG
TTGGCTCCTCTGTTGAAACTTGCTAGGGATTACAATGGATTTGACTCAATTCAAAGCTTTTATTCTCGTAAGAATTTCAC
AAAGTCTTCTCATCAAGGGTACCCACACTGGAATTTCCAGGAAGAAATAGAATTTCTTAATGCAGTTTTCCCAAATGGAG
CAGCATATTGTATGGGACGTGTGAATTCTGACTGTTGGTACTTGTATACTTTGGATTTTCCAGAGACTCAGGTAATCAGT
CAGCCAGATCAGACCCTGGAAATTCTGATCAGTGAGCTTGACCCAGCAGTTATGGACCAGTTCTACATGAAAGATGGTAT
TACTACAAAGGATGCCACTTGTGAGAGTGGAATTCGTGACGTGGTACCAGGTTCTGTCATTGATGCCACACTGTTCAATC
CTTGTGGGTATTCGATAAATGGAATGAAATCAGATAGAACTTATTGGACTATTCACATCACTCCAGAATCAGAATTTTCT
TATGTTAGCTTTGAAACAAACTTAAGTCAGACCTCCTATGATGACCTGGTCAGGAAAGTTGTAGAAGTCTTCAAGCCAGG
AAAATTTGTGACCACCCTGTTTGTAAATCAGAGTTCTAAATGTTGCACAGTGCTTTCTTCACCCCAGAAGATTGAAGGTT
TTAGATATTTTGCTTGCCAGAGCATTATGTTCAATGATTACAATTTTGTTTTTACCAGTTTTGCGAAGAAGCATCAACAA
CAGCAGAGT

Alignment

ORF - retro_fcat_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSEWDIL-LKDVQCSIISVTKTDKQEAYVLRCSESSMFVSKRRFILKTCGTTLLLKALVPLLKLARDYSG
          RSEWDIL.LKDVQCSIISVT.TDKQEAYVL..SESS.FVSKRRFILKT.GTTLLLK.L.PLLKLARDY.G
Retrocopy RSEWDIL>LKDVQCSIISVT-TDKQEAYVL--SESSTFVSKRRFILKTSGTTLLLKMLAPLLKLARDYNG

Parental  FDSIQSFFYSRKNFMKPSHQGYPHRNFQEEIEFLNAIFPNGAAYCMGRMNSDCWYLYTLDFPETRVISQP
          FDSIQSF.YSRKNF.K.SHQGYPH.NFQEEIEFLNA.FPNGAAYCMGR.NSDCWYLYTLDFPET.VISQP
Retrocopy FDSIQSF-YSRKNFTKSSHQGYPHWNFQEEIEFLNAVFPNGAAYCMGRVNSDCWYLYTLDFPETQVISQP

Parental  DQTLEILMSELDPAVMDQFYMKDGVTAKDVTRESGIRDLIPGSVIDATLFNPCGYSMNGMKSDGTYWTIH
          DQTLEIL.SELDPAVMDQFYMKDG.T.KD.T.ESGIRD..PGSVIDATLFNPCGYS.NGMKSD.TYWTIH
Retrocopy DQTLEILISELDPAVMDQFYMKDGITTKDATCESGIRDVVPGSVIDATLFNPCGYSINGMKSDRTYWTIH

Parental  ITPEPEFSYVSFETNLSQTSYDDLIRKVVEVFKPGKFVTTLFVNQSSKCRTVLSSPQKIEGFKRLDCQSA
          ITPE.EFSYVSFETNLSQTSYDDL.RKVVEVFKPGKFVTTLFVNQSSKC.TVLSSPQKIEGF....CQS.
Retrocopy ITPESEFSYVSFETNLSQTSYDDLVRKVVEVFKPGKFVTTLFVNQSSKCCTVLSSPQKIEGFRYFACQSI

Parental  MFNDYNFVFTSFAKKQQQQQS
          MFNDYNFVFTSFAKK.QQQQS
Retrocopy MFNDYNFVFTSFAKKHQQQQS

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	2.18 RPM	39.94 RPM
SRP017611_kidney	1.24 RPM	15.77 RPM
SRP017611_liver	1.01 RPM	18.40 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1175 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1175 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 18 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009171	9 retrocopies	retro_chof_1327, retro_chof_2200, retro_chof_238, retro_chof_2691, retro_chof_332, retro_chof_425, retro_chof_628, retro_chof_74, retro_chof_968,
Callithrix jacchus	ENSCJAG00000005257	6 retrocopies	retro_cjac_1600, retro_cjac_1738, retro_cjac_2452, retro_cjac_3020, retro_cjac_631, retro_cjac_850,
Dasypus novemcinctus	ENSDNOG00000006867	10 retrocopies	retro_dnov_1736, retro_dnov_1796, retro_dnov_185, retro_dnov_2436, retro_dnov_2653, retro_dnov_315, retro_dnov_357, retro_dnov_63, retro_dnov_752, retro_dnov_770,
Equus caballus	ENSECAG00000011198	4 retrocopies	retro_ecab_1110, retro_ecab_173, retro_ecab_57, retro_ecab_681,
Felis catus	ENSFCAG00000028033	1 retrocopy	retro_fcat_1175 ,
Homo sapiens	ENSG00000123505	5 retrocopies	retro_hsap_3315, retro_hsap_3630, retro_hsap_3922, retro_hsap_4917, retro_hsap_547,
Gorilla gorilla	ENSGGOG00000006466	5 retrocopies	retro_ggor_1304, retro_ggor_2448, retro_ggor_2640, retro_ggor_3070, retro_ggor_498,
Loxodonta africana	ENSLAFG00000013203	2 retrocopies	retro_lafr_1040, retro_lafr_770,
Macropus eugenii	ENSMEUG00000010630	1 retrocopy	retro_meug_1558,
Myotis lucifugus	ENSMLUG00000005666	4 retrocopies	retro_mluc_1675, retro_mluc_1687, retro_mluc_2625, retro_mluc_538,
Macaca mulatta	ENSMMUG00000000535	6 retrocopies	retro_mmul_1606, retro_mmul_1742, retro_mmul_1841, retro_mmul_2076, retro_mmul_2383, retro_mmul_2648,
Mus musculus	ENSMUSG00000075232	1 retrocopy	retro_mmus_47,
Nomascus leucogenys	ENSNLEG00000012818	4 retrocopies	retro_nleu_2758, retro_nleu_2983, retro_nleu_720, retro_nleu_812,
Otolemur garnettii	ENSOGAG00000030150	7 retrocopies	retro_ogar_1108, retro_ogar_1152, retro_ogar_1608, retro_ogar_1962, retro_ogar_3163, retro_ogar_354, retro_ogar_366,
Pongo abelii	ENSPPYG00000016924	4 retrocopies	retro_pabe_2977, retro_pabe_3194, retro_pabe_3826, retro_pabe_505,
Pan troglodytes	ENSPTRG00000018501	5 retrocopies	retro_ptro_2157, retro_ptro_2453, retro_ptro_2667, retro_ptro_3280, retro_ptro_411,
Rattus norvegicus	ENSRNOG00000000585	1 retrocopy	retro_rnor_1050,
Ictidomys tridecemlineatus	ENSSTOG00000000205	4 retrocopies	retro_itri_1402, retro_itri_1859, retro_itri_598, retro_itri_943,