RetrogeneDB ID: retro_rnor_2493

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:3136777..3137152(-)
• Located in intron of: ENSRNOG00000022943

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lamtor2
• Ensembl ID: ENSRNOG00000019908
• Aliases: Lamtor2, Mapbpip, RGD1562501, Robld3
• Description: mitogen-activated protein-binding protein-interacting protein [Source:RefSeq peptide;Acc:NP_001099911]

Sequence

>retro_rnor_2493
ATGCTGCGTCCTAAGGCTTTGATGCAGGTACTAAGCCAAGCCAACACTGGAGGAGTCCAAAGCACCCTGCTGCTGAATAA
TGAGGGATCGTTGCTGGCCTACTCCGATTATGGGGACACAGATGCCCAGGTCACCGCGGCCATCGCCAGTAACATCTGGG
CCGCATACGATAGGAACGGGAACCAAGCGTTTAATGAAGACAGTCTCAAATTTATCCTCATGGACTGCATGGAGGGCCGT
GTAGCCATTACCAGGGTGGCCAACCTTCTGCTATGTATGTATGCAGAGGAGACTGTAGGCTTCGGGATGCTCAAGGCCAA
GGCCCAGGCCTTGGTGCAGTACCTGGAGGAACCCCTCACCCAAGTAGCAGCCTCA

Alignment

ORF - retro_rnor_2493 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDSLK
          MLRPKAL.QVLSQANTGGVQSTLLLNNEGSLLAYS.YGDTDA.VTAAIASNIWAAYDRNGNQAFNEDSLK
Retrocopy MLRPKALMQVLSQANTGGVQSTLLLNNEGSLLAYSDYGDTDAQVTAAIASNIWAAYDRNGNQAFNEDSLK

Parental  FILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLTQVAAS
          FILMDCMEGRVAITRVANLLLCMYA.ETVGFGMLKAKAQALVQYLEEPLTQVAAS
Retrocopy FILMDCMEGRVAITRVANLLLCMYAEETVGFGMLKAKAQALVQYLEEPLTQVAAS

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	0.14 RPM	24.44 RPM
SRP017611_kidney	0.00 RPM	27.08 RPM
SRP017611_liver	0.27 RPM	20.31 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2493 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2493 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009193	1 retrocopy	retro_ecab_629,
Felis catus	ENSFCAG00000028596	1 retrocopy	retro_fcat_872,
Myotis lucifugus	ENSMLUG00000023871	1 retrocopy	retro_mluc_237,
Mus musculus	ENSMUSG00000028062	1 retrocopy	retro_mmus_878,
Otolemur garnettii	ENSOGAG00000016953	2 retrocopies	retro_ogar_2919, retro_ogar_910,
Pteropus vampyrus	ENSPVAG00000010328	1 retrocopy	retro_pvam_748,
Rattus norvegicus	ENSRNOG00000019908	3 retrocopies	retro_rnor_1037, retro_rnor_2493 , retro_rnor_847,
Tursiops truncatus	ENSTTRG00000013344	1 retrocopy	retro_ttru_1782,