RetrogeneDB ID: retro_rnor_2623

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:47358557..47359076(-)
• Located in intron of: ENSRNOG00000048658

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mettl9
• Ensembl ID: ENSRNOG00000025940
• Aliases: None
• Description: methyltransferase like 9 precursor [Source:RefSeq peptide;Acc:NP_001156636]

Sequence

>retro_rnor_2623
ACCCATAGACTTCTTGATTTAGGTGCTGGAGATGGAGAAGTCACAAAAATCATGAGCCCTCATTTTGAAGAAATTTATGC
CACTGAACTTTCTGAAACAATGATCTGGCAGCTCCAGAAGAAGAAATACAGAGTGCTTGGAATAAATGAATGGCAGAATA
CAGGGTTCCAGTATGATGTCATCAGCTGCTTAAATCTGCTGGATCGCTGTGATCAGCCCCTGGCATTGTTAAAAGATATC
AGAAGTGTCTTGGAGCCCACCCAAGGCAGGGTCATCCTGGCCTTGGTTTTGCCCTTTCATTCCTATGTGGAAAACGTAGG
TGGCAAGTGGGAGAAACCATCAGAAATTCTGGAAATCAAGGGACAGAATTGGGAAGAGCAAGTGAATAGCCTGCCTGAGG
TGTTCAGGAAAGCTGGCTTTGTCATCGAAGCTTTCACTAGACTGCCATACCTGTGTGAAGGTGACATGTACAATGACTAC
TATGTTCTGGACGACACTGTCTTTGTTCTCAGACCAGTG

Alignment

ORF - retro_rnor_2623 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.27 %
• Parental protein coverage: 54.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  THRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQLQKKKYRVLGINEWQNTGFQYDVISCLNLLDRC
          THRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQLQKKKYRVLGINEWQNTGFQYDVISCLNLLDRC
Retrocopy THRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQLQKKKYRVLGINEWQNTGFQYDVISCLNLLDRC

Parental  DQPLTLLKDIRSVLEPTQGRVILALVLPFHPYVENVGGKWEKPSEILEIKGQNWEEQVNSLPEVFRKAGF
          DQPL.LLKDIRSVLEPTQGRVILALVLPFH.YVENVGGKWEKPSEILEIKGQNWEEQVNSLPEVFRKAGF
Retrocopy DQPLALLKDIRSVLEPTQGRVILALVLPFHSYVENVGGKWEKPSEILEIKGQNWEEQVNSLPEVFRKAGF

Parental  VIEAFTRLPYLCEGDMYNDYYVLDDAVFVLRPV
          VIEAFTRLPYLCEGDMYNDYYVLDD.VFVLRPV
Retrocopy VIEAFTRLPYLCEGDMYNDYYVLDDTVFVLRPV

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	1.44 RPM	41.41 RPM
SRP017611_kidney	1.19 RPM	52.20 RPM
SRP017611_liver	0.81 RPM	23.73 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2623 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2623 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2623 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003533	2 retrocopies	retro_amel_402, retro_amel_704,
Canis familiaris	ENSCAFG00000017710	1 retrocopy	retro_cfam_1875,
Callithrix jacchus	ENSCJAG00000020564	1 retrocopy	retro_cjac_4083,
Mustela putorius furo	ENSMPUG00000016801	2 retrocopies	retro_mputfur_1323, retro_mputfur_1610,
Oryctolagus cuniculus	ENSOCUG00000004285	1 retrocopy	retro_ocun_754,
Otolemur garnettii	ENSOGAG00000008169	3 retrocopies	retro_ogar_1745, retro_ogar_307, retro_ogar_588,
Rattus norvegicus	ENSRNOG00000025940	1 retrocopy	retro_rnor_2623 ,
Sus scrofa	ENSSSCG00000030373	1 retrocopy	retro_sscr_441,
Tupaia belangeri	ENSTBEG00000003816	2 retrocopies	retro_tbel_1726, retro_tbel_2084,
Tursiops truncatus	ENSTTRG00000015624	4 retrocopies	retro_ttru_1100, retro_ttru_1466, retro_ttru_163, retro_ttru_467,