RetrogeneDB ID: retro_rnor_1378

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:1831978..1832669(-)
• Located in intron of: ENSRNOG00000014031

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rcc2
• Ensembl ID: ENSRNOG00000006327
• Aliases: None
• Description: Protein Rcc2 [Source:UniProtKB/TrEMBL;Acc:F1LVV4]

Sequence

>retro_rnor_1378
AAAATTGAAAGGTCTAAATGCAAGGGGCAGCTTTTGATCTTTTAAGCAACCAACTGTGACTTGATTGGACAGAAGGAAGT
GCCTAAACGGGAAGCTGCTTACTGTAACCTTTGTCAGAATTTTGGGGGTCCTGTACGTATGGGTGCTTGTCAGGAATCCA
GGTGCGAACCCTGGTTTCAGGTTCATGTGCTGCCCACAGTCTCCTTCTCATCACCACAGAATGGAAGCTGTGGAGCTGGG
GTTGAATGAAAAGGGGCAGCTGAGCCATGGTGATACCAAGAGGGTTGAATCTCCCCAGACTCATCGAGGCCCTCAGCCAT
GAGGCGATGGTGCTAATAGCATGTGGGCGCAGCCACACTCTGTGTTGACAGATACTGGCTGTGTGTTCGCCTTCGGAGAT
AATAAGATGGGGCAGCTGGGTCTCAGGAACCAGACAGATGCCATCCCAAGTCCTGCTCAGATGATGTACAACGGGCAGCC
AATTACCAACATGGCCTGCAGCACGGAATTCAGCATGCTGATGGACTGTAAAGAAAACCTCTGTTTCTTCTGGTGCCCTG
AATATGGCCATCTGGGACACAACTCAGATGGGAAGTTTATCACCCACATGCAGATGACAGAACATGATTGTGAGTTGGTG
CCTTAGAGAGTGGCCATCTTCATCAAGAAGACCAAGGACGGATCTTTCCTG

Alignment

ORF - retro_rnor_1378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.3 %
• Parental protein coverage: 53.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KLEGSKCKGQLLIFGATNWDLIGRKEVPKQQAAYRNLGQNLWGPHR-YGCLSGVRVRTVVSGSCAAHS-L
          K.E.SKCKGQLLIF.ATN.DLIG.KEVPK..AAY.NL.QN..GP.R.YGCLSG..VRT.VSGSCAAHS.L
Retrocopy KIERSKCKGQLLIF*ATNCDLIGQKEVPKREAAYCNLCQNFGGPVR<YGCLSGIQVRTLVSGSCAAHSLL

Parental  LITTEGKLWSW-GRNEKGQLGHGDTKRVEA-PRLIEALSHEAIVLAACGRNHTL-ALTDTGSVFAFGENK
          LITTE.KLWSW.G.NEKGQL.HGDTKRVE..PRLIEALSHEA.VL.ACGR.HTL..LTDTG.VFAFG.NK
Retrocopy LITTEWKLWSW<GLNEKGQLSHGDTKRVES>PRLIEALSHEAMVLIACGRSHTL<VLTDTGCVFAFGDNK

Parental  MGQLGLGNQTDAVPSPAQIMYNGQPITKMACGAEFSMLMDCKGNLYSFGCPEYGQLGHNSDGKFIARAQR
          MGQLGL.NQTDA.PSPAQ.MYNGQPIT.MAC..EFSMLMDCK.NL..F.CPEYG.LGHNSDGKFI...Q.
Retrocopy MGQLGLRNQTDAIPSPAQMMYNGQPITNMACSTEFSMLMDCKENLCFFWCPEYGHLGHNSDGKFITHMQM

Parental  IEYDCELVPRRVAIFIEKTKDGQIL
          .E.DCELVP.RVAIFI.KTKDG..L
Retrocopy TEHDCELVP*RVAIFIKKTKDGSFL

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	0.14 RPM	28.69 RPM
SRP017611_kidney	0.28 RPM	24.91 RPM
SRP017611_liver	0.20 RPM	11.36 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1378 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1378 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1378 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001396	1 retrocopy	retro_dnov_2692,
Homo sapiens	ENSG00000179051	3 retrocopies	retro_hsap_2677, retro_hsap_3073, retro_hsap_3597,
Gorilla gorilla	ENSGGOG00000015263	1 retrocopy	retro_ggor_2112,
Nomascus leucogenys	ENSNLEG00000007783	2 retrocopies	retro_nleu_2483, retro_nleu_298,
Otolemur garnettii	ENSOGAG00000014544	1 retrocopy	retro_ogar_2967,
Pongo abelii	ENSPPYG00000025834	3 retrocopies	retro_pabe_2547, retro_pabe_2957, retro_pabe_748,
Pan troglodytes	ENSPTRG00000000247	3 retrocopies	retro_ptro_1804, retro_ptro_2072, retro_ptro_2434,
Rattus norvegicus	ENSRNOG00000006327	1 retrocopy	retro_rnor_1378 ,
Rattus norvegicus	ENSRNOG00000050106	1 retrocopy	retro_rnor_2886,