RetrogeneDB ID: retro_mmus_1069

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:120046605..120047013(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ctdsp1
• Ensembl ID: ENSMUSG00000026176
• Aliases: Ctdsp1, GIP, NLIIF, Nif3, SCP1
• Description: CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1 [Source:MGI Symbol;Acc:MGI:2654470]

Sequence

>retro_mmus_1069
GACCAGAAGTCAGCAGTTTCCCAGAAGCCCCGGAGTCGGGGCATCCTCCACTCTCTCTTCTGCTGTGTCTGCCGGGATGA
TGGGGAGCCCCTACCTGCCCACAGTGGGGCTCCCCTGCTGGTGGAGGAAAATGGCGCCATCCCTAAGCACACCCCAGTCC
AGTACCTGCTTCCCGAGGCCAAGGCTCAGGACTCAGACAAGATCTGCGTAGTCATCGACCTGGACGAGACCCTGGTGCAC
AGCTCCTTCAAGCCAGTGAACAATGCGGACTTCATCATCCCGGTGGAGATAGATGGAGTGGTCCACCAGGTCTATGTGCT
GAAGCGGCCCCACGTAGATGAGTTCCTACAGCGAATGGGCAAGCTCTTTGAATGTGTGCTGTTCACTGCCAGCCTTGCCA
AGTACGCA

Alignment

ORF - retro_mmus_1069 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.26 %
• Parental protein coverage: 52.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DQKSAVSQKPRSRGILHSLFCCVCRDDGEPLPAHSGAPLLVEENGAIPKHTPVQYLLPEAKAQDSDKICV
          DQKSAVSQKPRSRGILHSLFCCVCRDDGEPLPAHSGAPLLVEENGAIPKHTPVQYLLPEAKAQDSDKICV
Retrocopy DQKSAVSQKPRSRGILHSLFCCVCRDDGEPLPAHSGAPLLVEENGAIPKHTPVQYLLPEAKAQDSDKICV

Parental  VIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYA
          VIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMG.LFECVLFTASLAKYA
Retrocopy VIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGKLFECVLFTASLAKYA

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
SRP007412_brain	0.00 RPM	17.20 RPM
SRP007412_cerebellum	0.00 RPM	22.10 RPM
SRP007412_heart	0.03 RPM	87.13 RPM
SRP007412_kidney	0.04 RPM	94.13 RPM
SRP007412_liver	0.03 RPM	101.70 RPM
SRP007412_testis	0.00 RPM	8.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1069 was not detected

EST

No EST(s) were mapped for retro_mmus_1069 retrocopy.

TSS

No TSS is located nearby retro_mmus_1069 retrocopy 5' end.

Lab

retro_mmus_1069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000026176	2 retrocopies	retro_mmus_1069 , retro_mmus_1156,
Mus musculus	ENSMUSG00000078429	1 retrocopy	retro_mmus_612,
Rattus norvegicus	ENSRNOG00000015295	2 retrocopies	retro_rnor_1573, retro_rnor_816,