RetrogeneDB ID: retro_rnor_1995

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:169035586..169036828(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000029080
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Shc1
• Ensembl ID: ENSRNOG00000020657
• Aliases: Shc1, P66shc
• Description: SHC-transforming protein 1 isoform a [Source:RefSeq peptide;Acc:NP_001157532]

Sequence

>retro_rnor_1995
TACATGAGTTGCGTGGAGGTCTTACAGTCAATGCGAGCCCTTGACTTCAATACCCGGACTCAGGTCACCAGGGAGGCCAT
CGGTTTGGTGTGTGAAGCTGTGCCTGGTGCCAAAGGGGCGACGACGAGGAGAAAGTCCTGCAGCCGCCCACTCAGCTCTA
TCCTGGGGAGGAGTAACCTGAAGTTTGCTGGAGTGCCGATCATTCTCACTGCGTCTACCAGCAGCCTAACCTCATGGCAG
CAGACCGCAAGCAGATCATTGCCAACCATCACATGCAATCTATCCCATTCGCGTCTGGTGGGAATCTGGACACAACTGAG
TACGTTGCCTATGTTGCCAAAGACCCTGCGAATCAGAGAGCCTGCCATATCCTGGAGTGTCCTGAAGGACTTGCTCAGGA
CGTCATCAGCACCATCGGGCAGGCCTTTGAGTTGCGCTTCAAACAGTATCTCAGGAATTCACCCAAGCTGGTCACCCCCC
ATGACAGGATGGCTGGCTTTGATGACTCAGCTTGGGATGAGGAGGAAGAAGAGCCCCCTGACCATCAGTACTACAATGAC
TTCCCAGGGAAGGAACCCCCTCCTGGTTGGAGTGGTAGATATGAGGCTTTGGGAAGGGGCTGCTCGACCCACTCTGCCCA
GTGCCCAAATGCACAGTCACTTGGGAGCTACACTGCCAATAGGGCAGCATGTTACAGGAGACCATGAAGTCCGTAAACAG
ATGCTGCCCCCACCACCGTGCCCAGGCAGAGAATTCTTCGATGATCCTTTCTATGTCAACATACAGAATCTAGACAAGGC
CCGGCAAGCTGGTGGTGGGGCCGGATCCCCAAATCCTTCTATTAATGGCAGTGCACCCCGAGACCTCTTTGACATGAAGC
CCTTTGAAGATACACTCCGTGTGCCGCCAGCTCCCCAGTCCATGTCCATGGCTGAGCAGCTCCAAGGGGAGTCCTGGTTT
CATGGGAAACTCAGCCGGCAGGAGTCTGAAGCGCTGCTGCAGCTCAACGGTGACTTCTTGGTGCGAGAGAGTACAACCAC
ACCTGGCCAGTACGTGCTCACTGGCCTGCAGAGGGGGCAGCCCAAGCACTTGCTTCTGGTGGACCCTGAAGGTGTGGTTC
AGACAAAGGATCACCGCTTTGAGAGTGTCAGTCACCTGATCAGCTACCACATGGACAATCACTTACCCATCATCTCTGCA
GGCAGCGAGCTGCGTCTACAGCAACCTTTGGATCTGAAAGTG

Alignment

ORF - retro_rnor_1995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.83 %
• Parental protein coverage: 88.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YMGCVEVLQSMRALDFNTRTQVTREAISLVCEAVPGAKGAMRRRKPCSRPLSSILGRSNLKFAGMPITLT
          YM.CVEVLQSMRALDFNTRTQVTREAI.LVCEAVPGAKGA..RRK.CSRPLSSILGRSNLKFAG.PI.LT
Retrocopy YMSCVEVLQSMRALDFNTRTQVTREAIGLVCEAVPGAKGATTRRKSCSRPLSSILGRSNLKFAGVPIILT

Parental  VSTSSL-NLMAADCKQIIANHHMQSISFASGGDPDTAEYVAYVAKDPVNQRACHILECPEGLAQDVISTI
          .STSSL.NLMAAD.KQIIANHHMQSI.FASGG..DT.EYVAYVAKDP.NQRACHILECPEGLAQDVISTI
Retrocopy ASTSSL<NLMAADRKQIIANHHMQSIPFASGGNLDTTEYVAYVAKDPANQRACHILECPEGLAQDVISTI

Parental  GQAFELRFKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQYYNDFPGKEPPLG-GVVDMRLREGAA
          GQAFELRFKQYLRN.PKLVTPHDRMAGFD.SAWDEEEEEPPDHQYYNDFPGKEPP.G.GVVDMRL.EGAA
Retrocopy GQAFELRFKQYLRNSPKLVTPHDRMAGFDDSAWDEEEEEPPDHQYYNDFPGKEPPPG>GVVDMRLWEGAA

Parental  RPTLPSTQMPSHLGATLPIGQHVTGDHEVRKQMLPPPPCPGRELFDDPSYVNIQNLDKARQAGGGAGPPN
          RPTLPS.QM.SHLGATLPIGQHVTGDHEVRKQMLPPPPCPGRE.FDDP.YVNIQNLDKARQAGGGAG.PN
Retrocopy RPTLPSAQMHSHLGATLPIGQHVTGDHEVRKQMLPPPPCPGREFFDDPFYVNIQNLDKARQAGGGAGSPN

Parental  PSVNGSAPRDLFDMKPFEDALRVPPAPQSMSMAEQLQGESWFHGKLSRREAEALLQLNGDFLVRESTTTP
          PS.NGSAPRDLFDMKPFED.LRVPPAPQSMSMAEQLQGESWFHGKLSR.E.EALLQLNGDFLVRESTTTP
Retrocopy PSINGSAPRDLFDMKPFEDTLRVPPAPQSMSMAEQLQGESWFHGKLSRQESEALLQLNGDFLVRESTTTP

Parental  GQYVLTGLQSGQPKHLLLVDPEGVVRTKDHRFESVSHLISYHMDNHLPIISAGSELCLQQPVDRKV
          GQYVLTGLQ.GQPKHLLLVDPEGVV.TKDHRFESVSHLISYHMDNHLPIISAGSEL.LQQP.D.KV
Retrocopy GQYVLTGLQRGQPKHLLLVDPEGVVQTKDHRFESVSHLISYHMDNHLPIISAGSELRLQQPLDLKV

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	13.80 RPM
SRP017611_kidney	0.00 RPM	48.15 RPM
SRP017611_liver	0.00 RPM	74.57 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1995 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1995 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1995 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000042626	1 retrocopy	retro_mmus_1687,
Rattus norvegicus	ENSRNOG00000020657	1 retrocopy	retro_rnor_1995 ,