RetrogeneDB ID: retro_rnor_232

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:24400006..24400384(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000013839
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Snrpd3
• Ensembl ID: ENSRNOG00000050410
• Aliases: None
• Description: small nuclear ribonucleoprotein D3 [Source:MGI Symbol;Acc:MGI:1914582]

Sequence

>retro_rnor_232
ATGTCTATTGGTAGGCCGATTGAAGTCCTGCAGGAAGCTCAAGGCTACATGGTAACACGTGAGACCATCACTGGTGAAGT
ATATCCAGGAAAGCTCATTGAGGCAGAGGACAACATGAACTGCCAGATGTCCAACATCACAGTCACATACAGAGATGGCC
CAGTGGCACAACCCGAGCAGGTATACATATGTGACACCAAGATCCGGTTTCCGATTTTGCCTAACATGCTGAAAAATGCA
CCCGTGTTAGAGAACCTGAAAAATAAAAACCAGGGCTCAAGAGCTGGCCAAGGAAAGGCTGCCATCTTGAAGGCCCAAGT
GGCTGCAAGAGGAAGAGGACATGAAATGGGGCCATGGAAACTTCCAGAAGCAAAGACA

Alignment

ORF - retro_rnor_232 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.49 %
• Parental protein coverage: 92.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRF
          MSIG.PI.VL.EA.G..VT.ET.TGEVY.GKLIEAEDNMNCQMSNITVTYRDG.VAQ.EQVYI...KIRF
Retrocopy MSIGRPIEVLQEAQGYMVTRETITGEVYPGKLIEAEDNMNCQMSNITVTYRDGPVAQPEQVYICDTKIRF

Parental  LILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMG
          .ILP.MLKNAP.L...KNKNQGS.AG.GKAAILKAQVAARGRG..MG
Retrocopy PILPNMLKNAPVLENLKNKNQGSRAGQGKAAILKAQVAARGRGHEMG

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	22.43 RPM
SRP017611_kidney	0.00 RPM	35.80 RPM
SRP017611_liver	0.00 RPM	12.71 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_232 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_232 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013864	1 retrocopy	retro_cfam_173,
Cavia porcellus	ENSCPOG00000012304	1 retrocopy	retro_cpor_297,
Dipodomys ordii	ENSDORG00000005801	1 retrocopy	retro_dord_791,
Otolemur garnettii	ENSOGAG00000012708	3 retrocopies	retro_ogar_1209, retro_ogar_2077, retro_ogar_2235,
Rattus norvegicus	ENSRNOG00000050410	1 retrocopy	retro_rnor_232 ,
Tarsius syrichta	ENSTSYG00000007649	1 retrocopy	retro_tsyr_1489,