RetrogeneDB ID: retro_rnor_1412

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:85083828..85084118(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ns5atp9
• Ensembl ID: ENSRNOG00000016561
• Aliases: None
• Description: PCNA-associated factor [Source:UniProtKB/Swiss-Prot;Acc:Q6RIA2]

Sequence

>retro_rnor_1412
GTGTGCACCAAAGCAAACTACATCCCTGGAGCCTGCAGAAAAATGGTGGCTTCTCAAGCCCCTCGGTTCTTGGCTCCTCC
ACCTTTGTCACGAATTCTTAAGGTTCGTTGAGAAAAGCTGAAAATAAGTATGCTGGAGGGAACCCAGTCTTTGTACGCCC
AACTCCCAAGTGGCAAAAAGGCATCGGGGACTTCTTCAGGCTGTCCCCTAAAGATTCTAAAAAGGAGAACCAGATTCCTG
AAGAAGCAGGAAGCAGTGGCTTAGGAGAAAAGCGTGTCCTTTGCAACCTG

Alignment

ORF - retro_rnor_1412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.0 %
• Parental protein coverage: 90.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRTKANYVPGAYRKVVASQ-APRKVLGSSTFVTNSSGSSRKAENKYAGGNPVCVRPTPKWQKGIGEFFRL
          V.TKANY.PGA.RK.VASQ..P..VLGSSTFVTNS.GS.RKAENKYAGGNPV.VRPTPKWQKGIG.FFRL
Retrocopy VCTKANYIPGACRKMVASQ<SP-SVLGSSTFVTNS*GSLRKAENKYAGGNPVFVRPTPKWQKGIGDFFRL

Parental  SPKDSKKENQIPEEAGSSGLGKAKRKACPL
          SPKDSKKENQIPEEAGSSGLG..KR..C.L
Retrocopy SPKDSKKENQIPEEAGSSGLGE-KRVLCNL

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	0.43 RPM
SRP017611_kidney	0.00 RPM	0.56 RPM
SRP017611_liver	0.00 RPM	0.54 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1412 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1412 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010763	2 retrocopies	retro_chof_1104, retro_chof_892,
Cavia porcellus	ENSCPOG00000006482	3 retrocopies	retro_cpor_138, retro_cpor_186, retro_cpor_365,
Dipodomys ordii	ENSDORG00000014912	1 retrocopy	retro_dord_674,
Monodelphis domestica	ENSMODG00000027710	2 retrocopies	retro_mdom_1275, retro_mdom_776,
Mus musculus	ENSMUSG00000040204	7 retrocopies	retro_mmus_1088, retro_mmus_1289, retro_mmus_1335, retro_mmus_1844, retro_mmus_2809, retro_mmus_2964, retro_mmus_378,
Otolemur garnettii	ENSOGAG00000003982	1 retrocopy	retro_ogar_501,
Rattus norvegicus	ENSRNOG00000016561	5 retrocopies	retro_rnor_1162, retro_rnor_1412 , retro_rnor_2595, retro_rnor_2624, retro_rnor_2698,
Ictidomys tridecemlineatus	ENSSTOG00000019643	4 retrocopies	retro_itri_1241, retro_itri_1324, retro_itri_1888, retro_itri_929,
Tupaia belangeri	ENSTBEG00000013732	2 retrocopies	retro_tbel_3099, retro_tbel_4093,