RetrogeneDB ID: retro_rnor_2137

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:35315819..35316650(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Bhmt
• Ensembl ID: ENSRNOG00000011200
• Aliases: None
• Description: Betaine--homocysteine S-methyltransferase 1 [Source:UniProtKB/Swiss-Prot;Acc:O09171]

Sequence

>retro_rnor_2137
ATCCAGGGTGGATCGAACGTCATGCAGACCTTCACTTTCTATGCAATTGAGGACAAGCTGGAAAACCGAGGGAACTCCGT
GGCAGAGAAGATATCTGGGCAGAAGGTCAATGAAGCTGCTTGTGACATTGCATGACAAGTTGCTGACGAAGGGGATGCGT
TGGTTGCAGGAGGCATGAGCCAGACACCTTCTTACCTTAGCTGCAGGAGTGAGACCGAAGTTAAAAAGATATTTCACCAA
CAGCTTGAGGTCTTCATGAAGATGAATGTGGACTTCCTCGTTGCAGAGTATGTTGAACATGTTGTAGCCGTGTGGGTAGT
AGAGGCCTTAAAAACACCAGGGAAGCCTATAGCAGCTACCACGTGCATCGGACCTGAAGGAGATCTACATGGCGTGTCTC
CTGGAGAGTGCGTGGTACATGTGGTGAAAGCAGGTGCCGCCATTGTCGGTGTGAACTTACACTTCTTCGACCCCAGCACC
AGCTTGCAGACAATAAAGCTCATGAAGGAGGGTTTGGAAACTGCTCGGCTGAAGGCTTACTTGATGAGCCAGCCCCTGGC
CAACCACACCCCTGACTGTGGCAAACAGGGATTTATTGATCTCCCAGAACTCGCCTTTGGATTGGAATCCAGAGTTGCTA
CCAGATGGGATACTCGAAAATACGCCAGAGAGGCCTACATCCCGAGGGTCAGGTACATTGGCGGCTGGTGAGGATTTGAA
CCCTACCACATCAGGGCTATTGCAGAGGAGCTGGCCCCAGAAAGGGGATTTTTGCCACCAGCTTCAGAAAAACATGGCAG
CTGGGGAAGTGGTTTGGACATGCACACCAAA

Alignment

ORF - retro_rnor_2137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.13 %
• Parental protein coverage: 68.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRAGSNVMQTFTFYASEDKLENRGNYVAEKISGQKVNEAACDIARQVADEGDALVAGGVSQTPSYLSCKS
          ...GSNVMQTFTFYA.EDKLENRGN.VAEKISGQKVNEAACDIA.QVADEGDALVAGG.SQTPSYLSC.S
Retrocopy IQGGSNVMQTFTFYAIEDKLENRGNSVAEKISGQKVNEAACDIA*QVADEGDALVAGGMSQTPSYLSCRS

Parental  ETEVKKIFHQQLEVFMKKNVDFLIAEYFEHVEEAVWAVEALKTSGKPIAATMCIGPEGDLHGVSPGECAV
          ETEVKKIFHQQLEVFMK.NVDFL.AEY.EHV..AVW.VEALKT.GKPIAAT.CIGPEGDLHGVSPGEC.V
Retrocopy ETEVKKIFHQQLEVFMKMNVDFLVAEYVEHVV-AVWVVEALKTPGKPIAATTCIGPEGDLHGVSPGECVV

Parental  RLVKAGAAIVGVNCHF-DPSTSLQTIKLMKEGLEAARLKAYLMSQPLAYHTPDCGKQGFIDLPEFPFGLE
          ..VKAGAAIVGVN.HF.DPSTSLQTIKLMKEGLE.ARLKAYLMSQPLA.HTPDCGKQGFIDLPE..FGLE
Retrocopy HVVKAGAAIVGVNLHFFDPSTSLQTIKLMKEGLETARLKAYLMSQPLANHTPDCGKQGFIDLPELAFGLE

Parental  PRVATRWDIQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTK
          .RVATRWD..KYAREAY...VRYIGG..GFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTK
Retrocopy SRVATRWDTRKYAREAYIPRVRYIGGW*GFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTK

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	3.02 RPM
SRP017611_kidney	0.00 RPM	31.96 RPM
SRP017611_liver	0.40 RPM	3450.90 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2137 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2137 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000007560	1 retrocopy	retro_cint_30,
Monodelphis domestica	ENSMODG00000019726	1 retrocopy	retro_mdom_1533,
Mus musculus	ENSMUSG00000074768	1 retrocopy	retro_mmus_192,
Rattus norvegicus	ENSRNOG00000011200	1 retrocopy	retro_rnor_2137 ,