RetrogeneDB ID: retro_mmus_986

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:3008717..3009493(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cox11
• Ensembl ID: ENSMUSG00000020544
• Aliases: None
• Description: cytochrome c oxidase assembly protein 11 [Source:MGI Symbol;Acc:MGI:1917052]

Sequence

>retro_mmus_986
ATGGGAGGGCTCTGGTGTCCGGAATGGAGGTTTGTAACTTTGTGTGGCCAGCGCTGGAGTCAGCCCTGATGGTCAGGGAG
GATTGTGGTGAACTCGGAGCTGATTCTTAGCCCCCCCCCCCCCCCCGGGTGGAGGAGTGGAGCCGGGACTGAGACGCTTG
GGGACATGGAAGCCCCTGAGCAAGCGCAGCCCAGAGTCCCACAGCCTGCCGCCTGCGCAGCCTTCAAAGTACCTGAGAAG
CAGCAACCCTTTCCAGTGCTCGCAGGAGGATGAGTGGCGGTGGAGGAACAAGACAGTGGTCACATATGTGGCCATGGCCG
CCGTGGGCATGCTAGGGGCCTCCTATGTCGCGGTGCCCCTTTATAGGCTCTACTGCCAGAATACTGGACTTGGAGGATCA
GCAGTGGCCGGGCACTCATCAGACCAGATTGAAAATAGGGTGCCTGTTAAGGATCGATCAGTAAAGTCACCTTTAATGTC
CGTTTCCAGTGGATCTTCAGACCTCAATGAACAGAGATCTATGTGGTACCAGTAGAGACTGCACTGGCATTTTATAAAGC
TAAAAATCCTACTAACAAACCAGTATTGTAATTTCTACATATAATGTTGTACCGTTTGAAGCTGGCCGATATTTCAATAA
AATACAGTGCTTCTGTTTTGAAGAACAAAGGCTTAATCCACAAGAAGAAGTGGATATGCCAGTGTTTTTCTACATTGACC
CTGAATTTGCAGAAGATCTGAGAATGGCGAATGTCGATCCCATTACTCTTTCTTAC

Alignment

ORF - retro_mmus_986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.41 %
• Parental protein coverage: 93.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGGLWCPGWRLVASCGRGWRQPGWSGRTVVNAELVLRPGWDGLGGAERGLRRLG-TWKRPCGVRGPATQ-
          MGGLWCP.WR.V..CG..W.QP.WSGR.VVN.EL.L............G...LG.TWK.P...R.P....
Retrocopy MGGLWCPEWRFVTLCGQRWSQP*WSGRIVVNSELILXXXXXXGWRSGAGTETLG>TWK-PLSKRSPESHS

Parental  -PPRRP----RSSNPFQRAQEDEWRRRNKTVLTYVAAAAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGH
          .PP..P....RSSNPFQ..QEDEWR.RNKTV.TYVA.AAVGMLGASY.AVPLYRLYCQ.TGLGGSAVAGH
Retrocopy LPPAQPSKYLRSSNPFQCSQEDEWRWRNKTVVTYVAMAAVGMLGASYVAVPLYRLYCQNTGLGGSAVAGH

Parental  SSDQIENMVPVKDR-VIKVTFNADVHASLQWNFRPQQTEIYVVPGETALAFYKAKNPTDKPV-IGISTYN
          SSDQIEN.VPVKDR...KVTFN.......QW.FRPQ.TEIYVVP.ETALAFYKAKNPT.KPV.I.ISTYN
Retrocopy SSDQIENRVPVKDR<ISKVTFN----VRFQWIFRPQ*TEIYVVPVETALAFYKAKNPTNKPV<IVISTYN

Parental  VVPFEAGQYFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFAEDPRMVNVDLITLSY
          VVPFEAG.YFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFAED.RM.NVD.ITLSY
Retrocopy VVPFEAGRYFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFAEDLRMANVDPITLSY

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	2.85 RPM
SRP007412_cerebellum	0.00 RPM	3.52 RPM
SRP007412_heart	0.06 RPM	6.79 RPM
SRP007412_kidney	0.00 RPM	5.06 RPM
SRP007412_liver	0.00 RPM	3.14 RPM
SRP007412_testis	0.09 RPM	4.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_986 was not detected

EST

No EST(s) were mapped for retro_mmus_986 retrocopy.

TSS

No TSS is located nearby retro_mmus_986 retrocopy 5' end.

Lab

retro_mmus_986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_986 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008482	1 retrocopy	retro_cpor_1340,
Dasypus novemcinctus	ENSDNOG00000014862	1 retrocopy	retro_dnov_1933,
Dipodomys ordii	ENSDORG00000001207	1 retrocopy	retro_dord_180,
Homo sapiens	ENSG00000166260	1 retrocopy	retro_hsap_3442,
Microcebus murinus	ENSMICG00000005225	1 retrocopy	retro_mmur_1119,
Monodelphis domestica	ENSMODG00000014855	1 retrocopy	retro_mdom_952,
Mus musculus	ENSMUSG00000020544	4 retrocopies	retro_mmus_1318, retro_mmus_2318, retro_mmus_2714, retro_mmus_986 ,
Nomascus leucogenys	ENSNLEG00000007990	1 retrocopy	retro_nleu_2297,
Ochotona princeps	ENSOPRG00000004138	1 retrocopy	retro_opri_441,
Pongo abelii	ENSPPYG00000008259	2 retrocopies	retro_pabe_156, retro_pabe_2847,
Pan troglodytes	ENSPTRG00000009422	1 retrocopy	retro_ptro_2335,
Rattus norvegicus	ENSRNOG00000046318	1 retrocopy	retro_rnor_1515,