RetrogeneDB ID: retro_rnor_2770

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:7844189..7845266(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046063
• 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_2770
GATTTTGGCTATGGAAAGGGGAAATGTACTAAACAAGGTCCGTCGGGAGCCCATGAGACGCGCTTTGGAGGTGACAAACT
TGAAGACCTTGAAGAAGCCAATCCATTCTCCTTCAAAGAGTTTTTGAAAACCAAGAACCTCAGCCTGTCAAAAGAAGACA
CAGCCACCAGTCGAATTTACCCGAAGGAGGCCTCGAGGCACCCACTGGGACTAGACCACAACTCCCCTGTCTCCCAGCCC
ATGGGATATGGCCTGGAATATCAGCAGCCATTTTTTGAAGACCCAACAAGAGCCAGCAACCTAGAGGAGGATGAAGAGGA
CGGGTGGAGCAGAGCCTACCTGCCGTCTGCCGTGGAGCAGACTCACTCCATGAGAGCCACGCAGAACTCATCGCCCTGTG
GCACCTACCTTTCCTTCTTTTCCAACGCGTCAGAGCTGGCAGGTCCTGAGTCTTTGCCCCCATGGACACTGAGTGACACT
GACTCCAGGCTCTCCCCAGCGTCTCCAGCTGGGAATCCTAATGTAGACTTTGCAGCTCATGAAGAATCCTTAGGGGACAG
ACACCTGCGGACGCTGCAGTTAAGTTACGAAGCACTGAAAGATGAAAACTCTAAGCTCAGAAGAAAGCTAAGTGAGGTTC
AGAGCTTCTCTGAAACTCAAACAAAAATGGTCAGGACGCTCGAACGGAAGTTGGAGGCGAAGATGATCAAGGAAGAGAGT
GACTTCCATGACCTGGAGTCAGTAGTCCAGCAAGTCGAACAGAACCTCGAACTGATGACCAAACGGGCTGTAAAAGCAGA
AAATCATGTCATGAAGCTGAAACAGGAAGTAAATTTGCTCCAGGCACAGCTCTCCAACTTCAAGCGAGAAAACGAAGCCC
TGCGGTCAGGCCAGGGTGCCAGCCTTACCGTGGTGAAGCAGAACACCGATGTGGCCTTGCAGAACCTCCATGTTGTCATG
AACAGTGCACACGCATCTATAAAGCAGCTGGTGTCTGGAGCAGAGACACTGAACCTTGTTGCTGAAATCCTCAAGTCTAT
CGACAGAATTACTGAAGTTAAGGATGAGGCAGACTCT

Alignment

ORF - retro_rnor_2770 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.44 %
• Parental protein coverage: 83.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFGYGKGKCTKQGPSGAHETRFGGDKLEDLEEANPFSFKEFLKTKNLSLSKEDTATSRIYPKEASRHPLG
          DFGYGKGKCTKQGPSGAHETRFGGDKLEDLEEANPFSFKEFLKTKNLSLSKEDTATSRIYPKEASRHPLG
Retrocopy DFGYGKGKCTKQGPSGAHETRFGGDKLEDLEEANPFSFKEFLKTKNLSLSKEDTATSRIYPKEASRHPLG

Parental  LDHNSPVSQPMGYGLEYQQPFFEDPTRASNLEEDEEDGWSRAYLPSAVEQTHSTRATQNSSPCGTYLSFF
          LDHNSPVSQPMGYGLEYQQPFFEDPTRASNLEEDEEDGWSRAYLPSAVEQTHS.RATQNSSPCGTYLSFF
Retrocopy LDHNSPVSQPMGYGLEYQQPFFEDPTRASNLEEDEEDGWSRAYLPSAVEQTHSMRATQNSSPCGTYLSFF

Parental  SNASELAGPESLPPWTLSDTDSRLSPASPAGNPNVDFAAHEESLGDRHLRTLQLSYEALKDENSKLRRKL
          SNASELAGPESLPPWTLSDTDSRLSPASPAGNPNVDFAAHEESLGDRHLRTLQLSYEALKDENSKLRRKL
Retrocopy SNASELAGPESLPPWTLSDTDSRLSPASPAGNPNVDFAAHEESLGDRHLRTLQLSYEALKDENSKLRRKL

Parental  SEVQSFSETQTEMVRTLERKLEAKMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVMKLKQEVNLL
          SEVQSFSETQT.MVRTLERKLEAKMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVMKLKQEVNLL
Retrocopy SEVQSFSETQTKMVRTLERKLEAKMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVMKLKQEVNLL

Parental  QAQLSNFKRENEALRSGQGASLTVVKQNTDVALQNLHVVMNSAHASIKQLVSGAETLNLVAEILKSIDRI
          QAQLSNFKRENEALRSGQGASLTVVKQNTDVALQNLHVVMNSAHASIKQLVSGAETLNLVAEILKSIDRI
Retrocopy QAQLSNFKRENEALRSGQGASLTVVKQNTDVALQNLHVVMNSAHASIKQLVSGAETLNLVAEILKSIDRI

Parental  TEVKDEADS
          TEVKDEADS
Retrocopy TEVKDEADS

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	0.07 RPM	42.49 RPM
SRP017611_kidney	0.21 RPM	36.15 RPM
SRP017611_liver	0.00 RPM	22.73 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2770 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2770 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2770 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 ,