RetrogeneDB ID: retro_rnor_816

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:80199782..80200367(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ctdsp1
• Ensembl ID: ENSRNOG00000015295
• Aliases: None
• Description: carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 [Source:RefSeq peptide;Acc:NP_001121551]

Sequence

>retro_rnor_816
AATGGCACCATCCCTAAGCATACCCCAGTCCAGCACCTGCTTCCCGAGGTCAAGGCCCAGGACTCAGACAAGATCTGCGT
TGTCATCGACCTGGACAAGACCCTGGTGCACAGCTCCTTCAAGCCAGTAAACAACGCTGACTTCATCATCCCAGTGGAGA
TTGATGGAGTGGTTCACCAGGTCTATGTACTGAAACGGCCCCACGTAGATGAGTTCCTACAGCGAATGGGCGAGCTCTTT
GAGTATGTGTTGTTCACTGCCCGTCTTGCCAAGTACGCAAACCCTGTAGCTGATCTGCTGGACAAGTGGGGAGCCTTCTG
TACCAGGCTGTTTTGAGAGTCCTGTGTCTTCCATCAGGGAAACTACGTAAAAGACCTGAGCAGGCTGGGCCGAGACCTGC
GGCGGGTGCTAATCTTAGACAACTCACCCGCCTCATACGTCTTTCATCCAGACAATGCCGTTCCAGTGGCCTCGTGGTTT
GATAACATGAGTGACACTGAGTTACACGATCTCTTACCCTTCTTTGAGCAACTCAGCCGCGTGGACGATGTATACTCAGT
GCTCAAACAGCCTAGGCCCGAGAGC

Alignment

ORF - retro_rnor_816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.85 %
• Parental protein coverage: 74.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGAIPKHTPVQYLLPEVKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVD
          NG.IPKHTPVQ.LLPEVKAQDSDKICVVIDLD.TLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVD
Retrocopy NGTIPKHTPVQHLLPEVKAQDSDKICVVIDLDKTLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVD

Parental  EFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILD
          EFLQRMGELFE.VLFTA.LAKYA.PVADLLDKWGAF..RLF.ESCVFH.GNYVKDLSRLGRDLRRVLILD
Retrocopy EFLQRMGELFEYVLFTARLAKYANPVADLLDKWGAFCTRLF*ESCVFHQGNYVKDLSRLGRDLRRVLILD

Parental  NSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLRQPRPGS
          NSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVL.QPRP.S
Retrocopy NSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLKQPRPES

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	32.71 RPM
SRP017611_kidney	0.00 RPM	179.90 RPM
SRP017611_liver	0.13 RPM	96.62 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_816 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_816 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000026176	2 retrocopies	retro_mmus_1069, retro_mmus_1156,
Rattus norvegicus	ENSRNOG00000015295	2 retrocopies	retro_rnor_1573, retro_rnor_816 ,