RetrogeneDB ID: retro_rnor_2914

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:40429304..40429897(-)
• 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_2914
ATGACCATCACTCAGTTTCCGTTATTTAAAGTTTGTACCTGCCTAGCAACAGTGTTCTCGTTCCTAAAGAGATTAATATG
CAGATCTGGCAGAGGAAGGAAATTGAGTGGAGACCAAATAATTTTGCCCACCACAGTTGATTATTCGTCTGTCCCTAAGC
AGACAGATGTGGAGGAGTGGACTTCCTGGGATGAAGATGTACCCACAAGCGTAAAGATCTAAGGAGGGAGTGGGAATGTG
GCAACACAGCAGAACTCTTTGGAACAACTGGAACCTGCCTATTTTAAGGACATGACACTAACTATATGGAAAACTCAGAA
AATTGTCATTACGAAGAGAGAACCACTGACTTTTGGTGTCCCAGATGGTAGTACAGGTTTTTCCAGTAGATTCTCAGCTA
CAGGAGATATGCCTTTTATTCATCCATCTTCAGAAGTAGGTGACTTAGATACGTGGCAAGAAAATAGCAATGCATGGGAG
AGGAAGAAGATGCAGCCTGGCAAGCAGAAGAAGTTCAGAGGCAGCAGAAAATTGCAGACAGAGAGAAGAGAGCAGCAGAA
CAACAAAGGAAGAAAATGGAGAACCAAGCGAAA

Alignment

ORF - retro_rnor_2914 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.94 %
• Parental protein coverage: 92.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAITQFRLFKVCTCLATVLSFLKRLICRSGRGRKLSGDQITLPTTVDYSSVPKQTDVEEWTSWDEDAPTS
          M.ITQF.LFKVCTCLATV.SFLKRLICRSGRGRKLSGDQI.LPTTVDYSSVPKQTDVEEWTSWDED.PTS
Retrocopy MTITQFPLFKVCTCLATVFSFLKRLICRSGRGRKLSGDQIILPTTVDYSSVPKQTDVEEWTSWDEDVPTS

Parental  VKIEGGTGNAAAQQNSLEQLEPDYFKDMTPTIRKTQKIVIKKREPLSFGVPDGSTGFSSRLAATQDMPFI
          VKI.GG.GN.A.QQNSLEQLEP.YFKDMT.TI.KTQKIVI.KREPL.FGVPDGSTGFSSR..AT.DMPFI
Retrocopy VKI*GGSGNVATQQNSLEQLEPAYFKDMTLTIWKTQKIVITKREPLTFGVPDGSTGFSSRFSATGDMPFI

Parental  HQSSELGDLDTWQENSNAWE-EEEDAAWQAEEVLRQQKIADREKRAAEQQRKKMEKEAQ
          H.SSE.GDLDTWQENSNAWE.EEEDAAWQAEEV.RQQKIADREKRAAEQQRKKME..A.
Retrocopy HPSSEVGDLDTWQENSNAWE<EEEDAAWQAEEVQRQQKIADREKRAAEQQRKKMENQAK

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_2914 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2914 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2914 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,