RetrogeneDB ID: retro_gacu_2

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXXI:2493485..2494517(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000002056
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: prmt1
• Ensembl ID: ENSGACG00000004897
• Aliases: None
• Description: protein arginine methyltransferase 1 [Source:ZFIN;Acc:ZDB-GENE-030131-693]

Sequence

>retro_gacu_2
ATGTCTCATGTCGTTAAGAAAAGAAAATTGGACAAAACCCGCCAGGAGCGCCTGTACTTCGACAGCTACACCGATGTGAC
CATCCACGAGGAGATGATAGCGGACCACGTCCGCACCAACACGTACCGGACGGCCATACTGCGGAACAGCGAGTCCATAC
GGGGCAAAGTCGTGCTGGACGTCGGGGCGGGCACCGGCGTGCTGAGCGTCTTCTGCGTCCAAGCCGGCGCGAGGAAGGTC
TACGCCGTGGAAGCCTGCTCCATCGCCGAGCAGGCGGTGAGAATAGTCCAGCAGAACAACATGGCGGACCGCATCGAGGT
CATCCGCGGCACGGTGGAGACGGTGGAGCTGCCGGAGAAGGTGGAGGTGATCGTGAGCGAGTGGATGGGCTACGCGCTGC
TGCACGAGTCCATGCTCAACTCGGTGCTCTACGCCCGCGACAAGTGGCTGAAGCCGGGCGGCGTCATCCTGCCCAGCAAA
GCCGAGCTCTACGTCGCGCCCATCGGCGACCCGGTGGTGGAGGAGCGCTTGAACTTCTGGTACACCGTCAAGGACCAGTA
CGGCGTGGACATGTCGTGCATGTCCGACTTCGCCAGGCGGTGCCTCATGAACACCGACATCACCGTCAGCTCGGTGACGG
TGGAGGACGTGCTCTCCCACCCGGCGCGCTTCGCCGAGCTCGACCTGTACTCGGTGACCGCGGAGCAGCTGCGCTCGGTG
CGCGGCGAGTTCCGGTGCGAGTCGTTCGGCTCGGCGGCGGTGAACGCCTTCTGCGTCTTCTTCACGGTGACCTTCCCGTG
CCCGGACCCGCCGCACGCGCTGCTGCTCTCCACGTCGCCGTTCAAGCCCGAGACGCACTGGAAGCAGGCGGTGCTGTACC
TGGACGCCCCCGTGGACGTGGTGCAGGACACGGCGGTCCGCGGGGAGATCAGCATGTTCCCCTCGGAGGAGAGCGCGCGG
CACATCTGCATCCACGTGGACTACGCCGTGGGCGAGCACAAGAGACAGTCCAAGACCTTCTCCATCCCCGAC

Alignment

ORF - retro_gacu_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.93 %
• Parental protein coverage: 51.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YFDSYAHFGIHEEMLKDEVRTLTYRNSMFHNKHLFKDKVVLDVGSGTGILCMFAAKAGAKKVIGIECSSI
          YFDSY....IHEEM..D.VRT.TYR.....N......KVVLDVG.GTG.L..F...AGA.KV...E..SI
Retrocopy YFDSYTDVTIHEEMIADHVRTNTYRTAILRNSESIRGKVVLDVGAGTGVLSVFCVQAGARKVYAVEACSI

Parental  SDYAVKIVKANKMDDVVTIIKGKVEEVDLPVEGVDIIISEWMGYCLFYESMLNTVIYARDKWLKPDGMIF
          ...AV.IV..N.M.D....I.G.VE.V.LP.E.V..I.SEWMGY.L..ESMLN.V.YARDKWLKP.G.I.
Retrocopy AEQAVRIVQQNNMADRIEVIRGTVETVELP-EKVEVIVSEWMGYALLHESMLNSVLYARDKWLKPGGVIL

Parental  PDRATLYVTAIEDRQYKDYKIHWW--ENVYGFDMSCIKEVA
          P..A.LYV..I.D.........W......YG.DMSC....A
Retrocopy PSKAELYVAPIGDPVVEERLNFWYTVKDQYGVDMSCMSDFA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_2 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_2 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003670	3 retrocopies	retro_cjac_1800, retro_cjac_1979, retro_cjac_764,
Danio rerio	ENSDARG00000010246	1 retrocopy	retro_drer_7,
Felis catus	ENSFCAG00000006081	1 retrocopy	retro_fcat_1762,
Homo sapiens	ENSG00000126457	1 retrocopy	retro_hsap_3406,
Gasterosteus aculeatus	ENSGACG00000004897	1 retrocopy	retro_gacu_2 ,
Gorilla gorilla	ENSGGOG00000000503	1 retrocopy	retro_ggor_2305,
Macaca mulatta	ENSMMUG00000003029	1 retrocopy	retro_mmul_2121,
Otolemur garnettii	ENSOGAG00000011938	2 retrocopies	retro_ogar_2471, retro_ogar_2929,
Rattus norvegicus	ENSRNOG00000026109	2 retrocopies	retro_rnor_1077, retro_rnor_2668,