RetrogeneDB ID: retro_mmus_736

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:87944402..87944811(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000044639
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2b
• Ensembl ID: ENSMUSG00000020390
• Aliases: Ube2b, 2610301N02Rik, E2-14k, HR6B, Rad6b, mHR6B
• Description: ubiquitin-conjugating enzyme E2B [Source:MGI Symbol;Acc:MGI:102944]

Sequence

>retro_mmus_736
GAGTTTGAGCGATTGCAAGAGGACCTACCTATGGAGTCAGTGGTGCACCATCTGAGAACATCATTGTGCAGTGTAATGCA
GGTATATTTGGACCAGACGGGACACCCTAAGGATGGTATATTTAAACTAGTAATAGAATTTCCTGAAGAATATCCAAATA
AGTCACCAACCATTAGGTTTTTATCCAGAATGTTTCATCCAAATGTGTATGCTGGTGGTAGCATATGTTTAGATATCCTT
GCAGAATGGATGGAGTCCCACATATGACTTCTCTTCCATCTTAATTTCAATTCAGTCTCTTTTGGATGAACTGAAACCAA
ACAGTCCAGTCAATAACCAAGCAACACAGCTTCATCAGAAGTACGAGGAGAGGGTTTCGGCCATTGTTGAGCAAAGCTGG
AATAATTCA

Alignment

ORF - retro_mmus_736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.31 %
• Parental protein coverage: 92.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DFKRLQEDPPV-GVSGAPSENNIMQWNAVIFGPE-GTPFEDGTFKLVIEFSEEYPNKPPTVRFLSKMFHP
          .F.RLQED.P..GVSGAPSEN.I.Q.NA.IFGP..G.P..DG.FKLVIEF.EEYPNK.PT.RFLS.MFHP
Retrocopy EFERLQEDLPM<GVSGAPSENIIVQCNAGIFGPD>GHP-KDGIFKLVIEFPEEYPNKSPTIRFLSRMFHP

Parental  NVYADGSICLDI-LQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQS
          NVYA.GSICLDI.LQN.WSPTYD.SSIL.SIQSLLDE..PNSP.N.QA.QL.Q.....YE.RVSAIVEQS
Retrocopy NVYAGGSICLDI>LQNGWSPTYDFSSILISIQSLLDELKPNSPVNNQATQLHQ----KYEERVSAIVEQS

Parental  WNDS
          WN.S
Retrocopy WNNS

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	102.59 RPM
SRP007412_cerebellum	0.00 RPM	61.44 RPM
SRP007412_heart	0.00 RPM	134.92 RPM
SRP007412_kidney	0.00 RPM	77.25 RPM
SRP007412_liver	0.00 RPM	61.66 RPM
SRP007412_testis	0.00 RPM	67.79 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_736 was not detected

EST

No EST(s) were mapped for retro_mmus_736 retrocopy.

TSS

No TSS is located nearby retro_mmus_736 retrocopy 5' end.

Lab

retro_mmus_736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_736 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001019	2 retrocopies	retro_cfam_2099, retro_cfam_216,
Dipodomys ordii	ENSDORG00000002525	1 retrocopy	retro_dord_646,
Echinops telfairi	ENSETEG00000006522	2 retrocopies	retro_etel_1531, retro_etel_771,
Macropus eugenii	ENSMEUG00000004740	1 retrocopy	retro_meug_718,
Myotis lucifugus	ENSMLUG00000012910	4 retrocopies	retro_mluc_1319, retro_mluc_1520, retro_mluc_2216, retro_mluc_478,
Monodelphis domestica	ENSMODG00000014209	1 retrocopy	retro_mdom_1218,
Mus musculus	ENSMUSG00000020390	1 retrocopy	retro_mmus_736 ,
Mus musculus	ENSMUSG00000060860	2 retrocopies	retro_mmus_1675, retro_mmus_3278,
Ochotona princeps	ENSOPRG00000006668	1 retrocopy	retro_opri_1186,
Pteropus vampyrus	ENSPVAG00000012430	1 retrocopy	retro_pvam_141,
Sarcophilus harrisii	ENSSHAG00000016143	2 retrocopies	retro_shar_12, retro_shar_173,
Tupaia belangeri	ENSTBEG00000010294	26 retrocopies	retro_tbel_2107, retro_tbel_2133, retro_tbel_2137, retro_tbel_2157, retro_tbel_2285, retro_tbel_2286, retro_tbel_2287, retro_tbel_2288, retro_tbel_2385, retro_tbel_2616, retro_tbel_2945, retro_tbel_3251, retro_tbel_3252, retro_tbel_3253, retro_tbel_3284, retro_tbel_3878, retro_tbel_4086, retro_tbel_4087, retro_tbel_4238, retro_tbel_4289, retro_tbel_4443, retro_tbel_4585, retro_tbel_4680, retro_tbel_4684, retro_tbel_4685, retro_tbel_4693,
Tarsius syrichta	ENSTSYG00000011148	2 retrocopies	retro_tsyr_151, retro_tsyr_553,
Tursiops truncatus	ENSTTRG00000016861	1 retrocopy	retro_ttru_700,