RetrogeneDB ID: retro_rnor_2811

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:66294901..66295117(+)
• Located in intron of: ENSRNOG00000021694

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atg12
• Ensembl ID: ENSRNOG00000000157
• Aliases: Atg12, Apg12l
• Description: Ubiquitin-like protein ATG12 [Source:UniProtKB/Swiss-Prot;Acc:Q2TBJ5]

Sequence

>retro_rnor_2811
TCTCCCATAATGAAAACAAAGAAATGGGCTGTGGAGCGGCCCCGGACCATACAAGCTCTCATCGACTTTATCAGAAAGTT
CCTCAGACTGCTGGTCTCGGAGCAGTTGTTTATTTATGTTGCCCCTTCCCCAGATCAAGAAGTTGGGACTCTATATGAGT
GTTCTGGCAGTGATGGTAAACTGGTCCTGCATTACTGCAAATCACAGGCATGGGGA

Alignment

ORF - retro_rnor_2811 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.16 %
• Parental protein coverage: 53.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TPIMKTKKWAVERTRTVQALIDFIRKFLRLLASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYC
          .PIMKTKKWAVER.RT.QALIDFIRKFLRLL.SEQLFIYV....APSPDQEVGTLYEC.GSDGKLVLHYC
Retrocopy SPIMKTKKWAVERPRTIQALIDFIRKFLRLLVSEQLFIYV----APSPDQEVGTLYECSGSDGKLVLHYC

Parental  KSQAWG
          KSQAWG
Retrocopy KSQAWG

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	56.94 RPM
SRP017611_kidney	0.00 RPM	43.06 RPM
SRP017611_liver	0.00 RPM	22.39 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2811 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2811 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004464	1 retrocopy	retro_chof_1745,
Cavia porcellus	ENSCPOG00000007187	2 retrocopies	retro_cpor_865, retro_cpor_944,
Equus caballus	ENSECAG00000012452	1 retrocopy	retro_ecab_883,
Echinops telfairi	ENSETEG00000018837	1 retrocopy	retro_etel_1721,
Homo sapiens	ENSG00000145782	1 retrocopy	retro_hsap_1860,
Gorilla gorilla	ENSGGOG00000016888	2 retrocopies	retro_ggor_1814, retro_ggor_2150,
Loxodonta africana	ENSLAFG00000015307	1 retrocopy	retro_lafr_450,
Myotis lucifugus	ENSMLUG00000002759	1 retrocopy	retro_mluc_2259,
Pongo abelii	ENSPPYG00000015699	3 retrocopies	retro_pabe_1518, retro_pabe_1519, retro_pabe_2158,
Pan troglodytes	ENSPTRG00000017154	2 retrocopies	retro_ptro_1240, retro_ptro_1748,
Rattus norvegicus	ENSRNOG00000000157	1 retrocopy	retro_rnor_2811 ,
Ictidomys tridecemlineatus	ENSSTOG00000011755	1 retrocopy	retro_itri_156,