RetrogeneDB ID: retro_drer_7

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 24:30278861..30279911(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDARG00000069706
• Aliases: prmt6, hrmt1l6, hrmt6, im:6908706
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: prmt1
• Ensembl ID: ENSDARG00000010246
• Aliases: prmt1, fb39h07, hrmt1l2, wu:fb39h07, zf1, zgc:66201
• Description: protein arginine methyltransferase 1 [Source:ZFIN;Acc:ZDB-GENE-030131-693]

Sequence

>retro_drer_7
ATGTCACAGCACGCTACCAAGAAACGAAAATTAGACAGAAGTACAGAGGATTACATGTACTTTGACAGCTACTCCGATGT
CACCATTCACGAAGAGATGATTGCAGACACGGTGCGCACGAACACCTACAGAATGGGCATTTTTAAAAACAGTAAGTCGA
TAGAGGGGAAAGTGGTGCTAGATGTGGGAGCCGGTACCGGCGTTTTGAGTTTATTCTGCGCCCAGGCAGGAGCCAGGAAA
GTGTATGCGGTGGAAGCGAGCTCGATTGCCGACCAGGCTGTGAAAATCGTAAAACTGAATCAGATGGAGGACAGAATCGA
AGTCATTAAATCAACACTAGAGACGATCGAACTAGCCGAAAAGGTGGATGTGATAGTCAGTGAATGGATGGGCTACGCGC
TCCTCCACGAATCCATGCTGAACTCTGTCATCTTTGCCCGGGATAAGTGGCTCAAACCCGGCGGCCTCATTTTGCCGAGC
CGCGCGGATCTTTACATCGCTCCCATCAACGACGTAGTGGTGGAGGGCAGGCTGGATTTCTGGAGCACCGTTAAAGGACA
GTACGGCGTGGACATGTCCTGCATGACCGACTTCGCCAGGAAGTGCATCATGAACAAAGACATCACCGTGAATCCGGTGA
CCGTGGAGGATGTGCTTTCCCACCCATGCAAATTCGCCGAGCTGGACTTGAACACGGTCACACTCGAGCAGCTCCGGGAT
GTGAACGGCTCGTTCAGCTGTTTGTGCTTCGGCTCGTCCTCCATCCACGCCTTCTGCGTGTGGTTCACTGTGACTTTCCC
AGCCGAGGAGAAGGCCCTGGTGCTCTCCACATCCCCGTTCAAAGCAGAGACCCACTGGAAACAGGCTGTGCTGTATCTGG
ACGATGCTGTGGACGTGATGCAGGACACTAAAGTCGAGGGCGAGATTAGTTTGTATCCCTCTGAGGAGAACTCGAGACAC
ATATGCATCCGCGTGGACTATGTGATAGGTGAACAGAAAAAGCACTCCAAAAGCTTTTCTATTCCTGACCAGTATTTAGA
AGTTAAATAA

Alignment

ORF - retro_drer_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.76 %
• Parental protein coverage: 56.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESSAKPAAEDMTSKDY-YFDSYAHFGIHEEMLKDEVRTLTYRNSMFHNKHLFKDKVVLDVGSGTGILCMF
          ....K....D....DY.YFDSY....IHEEM..D.VRT.TYR...F.N......KVVLDVG.GTG.L..F
Retrocopy QHATKKRKLDRSTEDYMYFDSYSDVTIHEEMIADTVRTNTYRMGIFKNSKSIEGKVVLDVGAGTGVLSLF

Parental  AAKAGAKKVIGIECSSISDYAVKIVKANKLDHIVTIIKGKVEEVELPVENVDIIISEWMGYCLFYESMLN
          .A.AGA.KV...E.SSI.D.AVKIVK.N........IK...E..EL..E.VD.I.SEWMGY.L..ESMLN
Retrocopy CAQAGARKVYAVEASSIADQAVKIVKLNQMEDRIEVIKSTLETIEL-AEKVDVIVSEWMGYALLHESMLN

Parental  TVIYARDKWLKPDGLIFPDRATLYVTAIEDRQYKDYKIHWWENV---YGFDMSCIKEVA
          .VI.ARDKWLKP.GLI.P.RA.LY...I.D..........W..V...YG.DMSC....A
Retrocopy SVIFARDKWLKPGGLILPSRADLYIAPIND-VVVEGRLDFWSTVKGQYGVDMSCMTDFA

Legend:

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

Expression

RNA-Seq

Danio rerio was not studied using RNA-Seq expression data.

ChIP-Seq

Danio rerio was not studied using ChIP-Seq data.

EST

8 EST(s) were mapped to retro_drer_7 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB365063	30278863	30279398	100	535	0	535
CD285311	30278845	30279404	99.2	554	5	549
CK682682	30278823	30279368	99.5	545	0	544
CK689918	30278975	30279290	95.6	305	9	294
CK712770	30278886	30279397	99.5	508	3	505
CO805740	30278836	30279045	98.1	203	4	197
EE214179	30278845	30279407	99.2	556	5	551
EE686346	30278908	30279427	95.4	492	8	472

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_7 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_7 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,