RetrogeneDB ID: retro_rnor_2980

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:128895545..128895919(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ebag9
• Ensembl ID: ENSRNOG00000004220
• Aliases: None
• Description: Receptor-binding cancer antigen expressed on SiSo cells [Source:UniProtKB/Swiss-Prot;Acc:Q5PQP2]

Sequence

>retro_rnor_2980
ATGACCTTCACTCAGTTTTGGTTATTTAATGTTTGTACCTGCCTAGCAACAGTGTTCTTGTTCCTAAAAGATTAATATGC
ACATCTGGCAGAGGAAGGAAATTAAGTGGAGACCAAATAACTTTGCCCACCACAGTTGATTATTCGTCTGTCCCTAAGCA
GTCAGACTGGAGGAGTGGACTTCCTGGGATGAAGATGTACCCACAAGTGTAAAAGATCTAAGGAGGGAATGGGAATGTGG
CAACGCAGCAGAACTCTTTGGAACAACCGGAACCTGACTATTTCAAGGACGTTACACCAACTATACAGAAAACTCAGAAA
ATTGTCATTAAGAAGAGAGAACCATTAAATTTTGGTGTCCCAGGTGGTAGCACA

Alignment

ORF - retro_rnor_2980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.81 %
• Parental protein coverage: 58.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAITQFRLFKVCTCLATVLSFLK-RLICRSGRGRKLSGDQITLPTTVDYSSVPKQTD-VEEWTSWDEDAP
          M..TQF.LF.VCTCLATV..FLK.RLIC.SGRGRKLSGDQITLPTTVDYSSVPKQ.D..EEWTSWDED.P
Retrocopy MTFTQFWLFNVCTCLATVFLFLK<RLICTSGRGRKLSGDQITLPTTVDYSSVPKQSD<LEEWTSWDEDVP

Parental  TSV-KIEGGTGNAAAQQNSLEQLEPDYFKDMTPTIRKTQKIVIKKREPLSFGVPDGST
          TSV.KI.GG.GN.A.QQNSLEQ.EPDYFKD.TPTI.KTQKIVIKKREPL.FGVP.GST
Retrocopy TSV>KI*GGNGNVATQQNSLEQPEPDYFKDVTPTIQKTQKIVIKKREPLNFGVPGGST

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	24.09 RPM
SRP017611_kidney	0.00 RPM	30.43 RPM
SRP017611_liver	0.00 RPM	18.62 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2980 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2980 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006190	1 retrocopy	retro_amel_1656,
Choloepus hoffmanni	ENSCHOG00000007848	5 retrocopies	retro_chof_1116, retro_chof_1455, retro_chof_1805, retro_chof_2245, retro_chof_751,
Cavia porcellus	ENSCPOG00000001059	1 retrocopy	retro_cpor_1185,
Dipodomys ordii	ENSDORG00000010177	2 retrocopies	retro_dord_418, retro_dord_91,
Equus caballus	ENSECAG00000009719	2 retrocopies	retro_ecab_211, retro_ecab_232,
Felis catus	ENSFCAG00000025490	1 retrocopy	retro_fcat_777,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Mus musculus	ENSMUSG00000022339	1 retrocopy	retro_mmus_3501,
Rattus norvegicus	ENSRNOG00000004220	2 retrocopies	retro_rnor_2914, retro_rnor_2980 ,
Sus scrofa	ENSSSCG00000006024	1 retrocopy	retro_sscr_569,
Ictidomys tridecemlineatus	ENSSTOG00000015326	1 retrocopy	retro_itri_1119,
Tursiops truncatus	ENSTTRG00000001745	2 retrocopies	retro_ttru_496, retro_ttru_672,