RetrogeneDB ID: retro_mmus_685

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:128550008..128550815(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gm129
• Ensembl ID: ENSMUSG00000038550
• Aliases: Ciart, Gm129
• Description: predicted gene 129 [Source:MGI Symbol;Acc:MGI:2684975]

Sequence

>retro_mmus_685
ATGGATTCTCCATCTAGTGTTTCTTCTTATTCCTCCTCCTCCCTCTCCCCATCATTTTCTATGTCCCCTGTGAACAGTGA
CTTTAGCTTCCCTTCTGATAACGAGAGGGAGGGCAAGGGCACCCGTGAGCTCAGGCCAGACACTGTGGGTCAGAGAGGAG
GTTCCAGGCCCAGTCCAGGCCCTGTCCGCTGCAGACATCGACCCAGGGTTTCTAGTAACCAACATACAGCACCGCATCTG
GAACAGCAAGGATCTGAAGTCAAGAGATCAAGAGACGGTGAACTGGAGATGAGTCTGAACACCCAAGGATGTACTACAGA
GGGAGATCTGCTCTTTGCTCAAAAGTGTAAAGAACTCCAAGGGTTCATAGGGCCCCTCACAGACCTACTGAATGGACTCA
AGATGGGTCGCTTTGACAGAGGATTAAGTAGCTTCCAACAGAGTGTGGCCATGGACCGGATCCAGCGCATAGTGGGTGTT
TTACAGAAGCCTCAGATGGGAGAACGTTATCTAGGAACCTTGCTGCAGGTGGAAGGGATGTTAAAGACTTGGTTTCCTCA
CATAGCTGCCCAGAAATCATCCTCAGGAAGTAGCAGGCACCAGATAAGCAAGCACTTTTCCAGTCACCACAGTGACCCGG
GGGCTGCTTTTCCTGCACCTCTCCTAGAGAAGATGGGCCAAACACAGCTGGGACATTTAGTTTTGAAACCAAAGCATCCT
TGGCATCTCACAGGATGGCCAGCTATGAACCTCACTTGGATTCATAGCACTCCAATTTGTAACCCTCCCCTCAGTTCCCA
AGGCTCC

Alignment

ORF - retro_mmus_685 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.54 %
• Parental protein coverage: 71.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSPSSVSSYSSSSLSPSFSTSSVNSDFSFPSDNEREGKGTHELRPDTVGQRGGSRPSPGPIRCRHRPRV
          MDSPSSVSSYSSSSLSPSFS.S.VNSDFSFPSDNEREGKGT.ELRPDTVGQRGGSRPSPGP.RCRHRPRV
Retrocopy MDSPSSVSSYSSSSLSPSFSMSPVNSDFSFPSDNEREGKGTRELRPDTVGQRGGSRPSPGPVRCRHRPRV

Parental  SSNQHTAPHLEQQGSEVKRSRDGEQETSLNTQGCTTEGDLLFAQKCKELQGFIRPLTDLLNGLKMGRFDR
          SSNQHTAPHLEQQGSEVKRSRDGE.E.SLNTQGCTTEGDLLFAQKCKELQGFI.PLTDLLNGLKMGRFDR
Retrocopy SSNQHTAPHLEQQGSEVKRSRDGELEMSLNTQGCTTEGDLLFAQKCKELQGFIGPLTDLLNGLKMGRFDR

Parental  GLSSFQQSVAMDRIQRIVGVLQKPQMGERYLGTLLQVEGMLKTWFPHIAAQKSSSGGSRHQISKHFPSHH
          GLSSFQQSVAMDRIQRIVGVLQKPQMGERYLGTLLQVEGMLKTWFPHIAAQKSSSG.SRHQISKHF.SHH
Retrocopy GLSSFQQSVAMDRIQRIVGVLQKPQMGERYLGTLLQVEGMLKTWFPHIAAQKSSSGSSRHQISKHFSSHH

Parental  GDPGAASPAPLLEKMGQTQLGHLVLKPKQPWHLTGWPAMNLTWIHSTPICNPPLSSQGS
          .DPGAA.PAPLLEKMGQTQLGHLVLKPK.PWHLTGWPAMNLTWIHSTPICNPPLSSQGS
Retrocopy SDPGAAFPAPLLEKMGQTQLGHLVLKPKHPWHLTGWPAMNLTWIHSTPICNPPLSSQGS

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	0.02 RPM	14.93 RPM
SRP007412_cerebellum	0.13 RPM	19.63 RPM
SRP007412_heart	0.00 RPM	9.25 RPM
SRP007412_kidney	0.06 RPM	11.65 RPM
SRP007412_liver	0.03 RPM	35.56 RPM
SRP007412_testis	0.00 RPM	7.82 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_685 was not detected

EST

No EST(s) were mapped for retro_mmus_685 retrocopy.

TSS

No TSS is located nearby retro_mmus_685 retrocopy 5' end.

Lab

retro_mmus_685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_685 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008999	1 retrocopy	retro_chof_2196,
Monodelphis domestica	ENSMODG00000018781	1 retrocopy	retro_mdom_1179,
Mus musculus	ENSMUSG00000038550	1 retrocopy	retro_mmus_685 ,