RetrogeneDB ID: retro_mmus_1536

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:91513215..91514260(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084301
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cdc20
• Ensembl ID: ENSMUSG00000006398
• Aliases: Cdc20, 2310042N09Rik, C87100, p55CDC
• Description: cell division cycle 20 [Source:MGI Symbol;Acc:MGI:1859866]

Sequence

>retro_mmus_1536
AGGCTCAGCGGCAAACCTCAGAATGCCCCAGAAGGCTACCAGAACAGACTGAAAGCACTCTACAGCCAGAAAGGCACGCC
TGGCTCCAGCAGGAAGGCTTGCAGATGCATCCCTTCTCTGCCAGACAGGAATCTTGATGCCCCCGAAATCCGGAATGACT
ACTACCTGAATTTTGTAGATTGGAGCTCTGGAAATGTATTGGCTGTGGCACTGGACAACAGTGTGTACTTATGGAACGCT
GGTTCTGGTGACATCCTGCAGTTGTTGCAAATGGAGCAGCCTGGGGGCTACATATCCTCGGTGGCCTGGATCAAGGAGGG
CAACTACCTAGCTGTGGGCACCAGCAATGCTGAGGTGCAGTTATGGGATGTGCAGCAGCAGAAATGACTTCGAAACATGA
CCTGTCACTCCGCTCAAGTAAGCTCTCTCAGTTGGAACAGCTATATCCTGTCCAGTGGTTCACGGTCTGGCCACATCCAC
CACCATGATGTTCGGGTAGCAGAACACCATGTGGCCACACTGAGTGGCCATAGCCAGGAAGTATGTGGGCTTCGCTGGGC
CCCAGGATAGACGACACCTGGCAAGTGGTGGCAATGATAACATTGTCAACGTGTGGCCCAGTGGTCCTGGAGAAAGTGGA
TGGGCTCCCCTGCAAATATTCACTCAACATCAAGGTGCTGTCAAGGCTGTTGCATGGTGTCCCTGGCAGTCCAATATCCT
GGCAACAGGAGGAGGAACCAGTGACCGGCACATTTGCATTTGGAACGTCTGCTCAGGGGCCTGTCTGAGTGCTGTGGAGG
TGCATTCCCAGGTGTGCTCTGTCCACTGATCTCCCCAACATAAGGAGCTGATCTCAGGTCACGGCTTTGCCCAGAACCAG
CTGGGTATTTGGAAGTATCCAACCATGGCCAAGGTGGCTGAGCTCAAAAGTCACACAGCACGGGTCCTGGGTCTTACAAT
GAGTCCAAATGGGGCCACAGTGGCATCAGCAGCAGCTGACGAGACTCTACAGTTGTGGCGCTGCTTTGAGATGGACCCTG
CCCTT

Alignment

ORF - retro_mmus_1536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.12 %
• Parental protein coverage: 69.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLSGKPQNAPEGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVA
          RLSGKPQNAPEGYQNRLK.LYSQK.TPGSSRK.CR.IPSLPDR.LDAPEIRNDYYLN.VDWSSGNVLAVA
Retrocopy RLSGKPQNAPEGYQNRLKALYSQKGTPGSSRKACRCIPSLPDRNLDAPEIRNDYYLNFVDWSSGNVLAVA

Parental  LDNSVYLWNAGSGDILQLLQMEQPGDYISSVAWIKEGNYLAVGTSNAEVQLWDVQQQKRLRNMTSHSARV
          LDNSVYLWNAGSGDILQLLQMEQPG.YISSVAWIKEGNYLAVGTSNAEVQLWDVQQQK.LRNMT.HSA.V
Retrocopy LDNSVYLWNAGSGDILQLLQMEQPGGYISSVAWIKEGNYLAVGTSNAEVQLWDVQQQK*LRNMTCHSAQV

Parental  SSLSWNSYILSSGSRSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWAP-DGRHLASGGNDNIVNVWPSGP
          SSLSWNSYILSSGSRSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWAP.D.RHLASGGNDNIVNVWPSGP
Retrocopy SSLSWNSYILSSGSRSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWAP>DRRHLASGGNDNIVNVWPSGP

Parental  GESGWAPLQTFTQHQGAVKAVAWCPWQSNILATGGGTSDRHIRIWNVCSGACLSAVDVHSQVCSILWSPH
          GESGWAPLQ.FTQHQGAVKAVAWCPWQSNILATGGGTSDRHI.IWNVCSGACLSAV.VHSQVCS...SP.
Retrocopy GESGWAPLQIFTQHQGAVKAVAWCPWQSNILATGGGTSDRHICIWNVCSGACLSAVEVHSQVCSVH*SPQ

Parental  YKELISGHGFAQNQLVIWKYPTMAKVAELKGHTARVLGLTMSPDGATVASAAADETLRLWRCFEMDPAL
          .KELISGHGFAQNQL.IWKYPTMAKVAELK.HTARVLGLTMSP.GATVASAAADETL.LWRCFEMDPAL
Retrocopy HKELISGHGFAQNQLGIWKYPTMAKVAELKSHTARVLGLTMSPNGATVASAAADETLQLWRCFEMDPAL

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	0.51 RPM
SRP007412_cerebellum	0.00 RPM	1.56 RPM
SRP007412_heart	0.00 RPM	1.37 RPM
SRP007412_kidney	0.02 RPM	1.31 RPM
SRP007412_liver	0.00 RPM	0.41 RPM
SRP007412_testis	0.14 RPM	97.52 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1536 was not detected

EST

No EST(s) were mapped for retro_mmus_1536 retrocopy.

TSS

No TSS is located nearby retro_mmus_1536 retrocopy 5' end.

Lab

retro_mmus_1536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1536 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006680	2 retrocopies	retro_chof_2172, retro_chof_2286,
Callithrix jacchus	ENSCJAG00000003414	1 retrocopy	retro_cjac_1608,
Homo sapiens	ENSG00000117399	1 retrocopy	retro_hsap_4187,
Gorilla gorilla	ENSGGOG00000010419	1 retrocopy	retro_ggor_96,
Mus musculus	ENSMUSG00000006398	1 retrocopy	retro_mmus_1536 ,
Nomascus leucogenys	ENSNLEG00000013419	1 retrocopy	retro_nleu_2847,
Pongo abelii	ENSPPYG00000001448	1 retrocopy	retro_pabe_3428,
Pan troglodytes	ENSPTRG00000000634	1 retrocopy	retro_ptro_2843,
Tarsius syrichta	ENSTSYG00000012703	3 retrocopies	retro_tsyr_1560, retro_tsyr_442, retro_tsyr_938,
Tursiops truncatus	ENSTTRG00000010813	1 retrocopy	retro_ttru_1309,