RetrogeneDB ID: retro_rnor_1215

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:18258856..18259864(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000048427
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sdccag3
• Ensembl ID: ENSRNOG00000018876
• Aliases: None
• Description: serologically defined colon cancer antigen 3 [Source:RefSeq peptide;Acc:NP_001013153]

Sequence

>retro_rnor_1215
GGTGACAAACTTGAAGACCTTGAAGAAGCCAATCCATTCTCCTTCAAAGAGTTTTTGAAAACCAAGAACCTCAGCCTGTC
AAAAGAAGACACAGCCACCAGTCGAATTTACCCGAAGGAGGCCTCGAGGCACCCACTGGGACTAGACCACAACTCCCCTG
TCTCCCAGCCCATGGGATATGGCCTGGAATATCAGCAGCCATTTTTTGAAGACCCAACAAGAGCCAGCAACCTAGAGGAG
GATGAAGAGGACGGGTGGAGCAGAGCCTACCTGCCGTCTGCCGTGGAGCAGACTCACTCCACGAGAGCCACGCAGAACTC
ATCGCCCTGTGGCACCTACCTTTCCTTCTTTTCCAACGCGTCAGAGCTGGCAGGTCCTGAGTCTTTGCCCCCATGGACAC
TGAGTGACACTGACTCCAGGCTCTCCCCAGCGTCTCCAGCTGGGAATCCTAATGTAGACTTTGCAGCTCATGAAGAATCC
TTAGGGGACAGACACCTGCGGACGCTGCAGTTAAGTTACGAAGCACTGAAAGATGAAAACTCTAAGCTCAGAAGAAAGCT
AAGTGAGGTTCAGAGCTTCTCTGAAACTCAAACAGAAATGGTGAGGACGCTCGAACGGAAGTTGGAGGCGAAGATGATCA
AGGAAGAGAGTGACTTCCATGACCTGGAGTCAGTAGTCCAGCAAGTCGAACAGAACCTCGAACTGATGACCAAACGGGCT
GTAAAAGCAGAAAATCATGTCATGAAGCTGAAACAGGAAGTAAATTTGCTCCAGGCACAGCTCTCCAACTTCAAGCGAGA
AAACGAAGCCCTGCGGTCAGGCCAGGGTGCCAGCCTTACCGTGGTGAAGCAGAACACCGATGTGGCCTTGCAGAACCTCC
ATGTTGTCATGAACAGTGCACACGCATCTATAAAGCAGCTGGTGTCTGGAGCAGAGACACTGAACCTTGTTGCTGAAATC
CTCAAGTCTATCGACAGAATTACTGAAGTTAAGGATGAGGCAGACTCT

Alignment

ORF - retro_rnor_1215 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDKLEDLEEANPFSFKEFLKTKNLSLSKEDTATSRIYPKEASRHPLGLDHNSPVSQPMGYGLEYQQPFFE
          GDKLEDLEEANPFSFKEFLKTKNLSLSKEDTATSRIYPKEASRHPLGLDHNSPVSQPMGYGLEYQQPFFE
Retrocopy GDKLEDLEEANPFSFKEFLKTKNLSLSKEDTATSRIYPKEASRHPLGLDHNSPVSQPMGYGLEYQQPFFE

Parental  DPTRASNLEEDEEDGWSRAYLPSAVEQTHSTRATQNSSPCGTYLSFFSNASELAGPESLPPWTLSDTDSR
          DPTRASNLEEDEEDGWSRAYLPSAVEQTHSTRATQNSSPCGTYLSFFSNASELAGPESLPPWTLSDTDSR
Retrocopy DPTRASNLEEDEEDGWSRAYLPSAVEQTHSTRATQNSSPCGTYLSFFSNASELAGPESLPPWTLSDTDSR

Parental  LSPASPAGNPNVDFAAHEESLGDRHLRTLQLSYEALKDENSKLRRKLSEVQSFSETQTEMVRTLERKLEA
          LSPASPAGNPNVDFAAHEESLGDRHLRTLQLSYEALKDENSKLRRKLSEVQSFSETQTEMVRTLERKLEA
Retrocopy LSPASPAGNPNVDFAAHEESLGDRHLRTLQLSYEALKDENSKLRRKLSEVQSFSETQTEMVRTLERKLEA

Parental  KMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVMKLKQEVNLLQAQLSNFKRENEALRSGQGASLT
          KMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVMKLKQEVNLLQAQLSNFKRENEALRSGQGASLT
Retrocopy KMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVMKLKQEVNLLQAQLSNFKRENEALRSGQGASLT

Parental  VVKQNTDVALQNLHVVMNSAHASIKQLVSGAETLNLVAEILKSIDRITEVKDEADS
          VVKQNTDVALQNLHVVMNSAHASIKQLVSGAETLNLVAEILKSIDRITEVKDEADS
Retrocopy VVKQNTDVALQNLHVVMNSAHASIKQLVSGAETLNLVAEILKSIDRITEVKDEADS

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	1.51 RPM	42.49 RPM
SRP017611_kidney	0.98 RPM	36.15 RPM
SRP017611_liver	0.74 RPM	22.73 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1215 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1215 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000165689	1 retrocopy	retro_hsap_1944,
Gorilla gorilla	ENSGGOG00000010905	1 retrocopy	retro_ggor_1414,
Mus musculus	ENSMUSG00000026927	3 retrocopies	retro_mmus_1545, retro_mmus_3492, retro_mmus_711,
Nomascus leucogenys	ENSNLEG00000008186	1 retrocopy	retro_nleu_891,
Otolemur garnettii	ENSOGAG00000015872	1 retrocopy	retro_ogar_3418,
Pongo abelii	ENSPPYG00000019772	2 retrocopies	retro_pabe_1612, retro_pabe_256,
Pan troglodytes	ENSPTRG00000021555	1 retrocopy	retro_ptro_1300,
Rattus norvegicus	ENSRNOG00000018876	2 retrocopies	retro_rnor_1215 , retro_rnor_2770,