RetrogeneDB ID: retro_rnor_1573

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:225128785..225129383(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000037161
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1573
CTGGTGGAGGAAAATGGTGCCATCCCTAAGCATACCCCAGTCCAGTACCTGCTTCCCGAGGTCAAGCCCCAGGACTCAGA
CAAGATCTGCGTTGTCATCGACCTGGACGAGACCCTGGTTGCACAGCTCCTTCAAGCCAGTAAACAACACTGACTTCATC
ATCCCAGTGGAGATTGATGGAGTGGTTCACCAGGTCTATGTACTGAAACGGCCCCACGTAGATGAGTTCCTACAGCGAAT
GGGCGAGCTCTTTGAGAGTGTGTTGTTCACTGCCAGTCTTGCCAGGTACGCAAACCCTGTAGCTGATCTGCTGGACAAGT
GGGGAGCCTTCCGTGCCAAGCTGTTTCGAGAGTCCTGTGTCTTCCATCGGGGAAACTACGTAAAGGACCTGAGCAGGCTG
GGCCGAGACCTGCGGCGGGTGCTAATCTTAGACAACTCACCCGCCTCATACGTCTTCCATCCAGACAATGCCGTTCCAGT
GGCCTCGTGGGTTGACAACATGAGTGACACTGAGTTACACGATCTCTTACCCTTCTTTGAGCAACTCATCTGCGTGGACA
ACGTGTACTCAGTGCTCAGACAGCCTAGGCCCAAGAGC

Alignment

ORF - retro_rnor_1573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94. %
• Parental protein coverage: 76.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVEENGAIPKHTPVQYLLPEVKAQDSDKICVVIDLDETLV-HSSFKPVNNADFIIPVEIDGVVHQVYVLK
          LVEENGAIPKHTPVQYLLPEVK.QDSDKICVVIDLDETLV.HSSFKPVNN.DFIIPVEIDGVVHQVYVLK
Retrocopy LVEENGAIPKHTPVQYLLPEVKPQDSDKICVVIDLDETLV>HSSFKPVNNTDFIIPVEIDGVVHQVYVLK

Parental  RPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRR
          RPHVDEFLQRMGELFE.VLFTASLA.YA.PVADLLDKWGAFRA.LFRESCVFHRGNYVKDLSRLGRDLRR
Retrocopy RPHVDEFLQRMGELFESVLFTASLARYANPVADLLDKWGAFRAKLFRESCVFHRGNYVKDLSRLGRDLRR

Parental  VLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLRQPRPGS
          VLILDNSPASYVFHPDNAVPVASW.DNMSDTELHDLLPFFEQL..VD.VYSVLRQPRP.S
Retrocopy VLILDNSPASYVFHPDNAVPVASWVDNMSDTELHDLLPFFEQLICVDNVYSVLRQPRPKS

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	0.00 RPM	96.62 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1573 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1573 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1573 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,