RetrogeneDB ID: retro_mmus_2714

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:3207868..3208704(+)
• 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_2714
ATGGGAGGGCTCTGGTGTCCAGACTGGAGGTTTGTAACTTTGTGTGGCCAACGCTGGAATCAGCCCTGATGGTCAGGGAG
GATTGGGATGAACTCGGAGCTGATTCTTAGGCCCCCCGGGTGGAAAGAGCTCGGGGGAGTGGAGCCGGGACTGAGATGCC
TGGGGACATGGAAGCGCCTGAGCGAGTGCAGCCCAGAGTCCCACAGCCTGCCGCCTGCGCAGCCTTCAAGGTAGCTGAGA
AGCAGCAACCCTTTCCAGTGCTCGCAGGAGGACAAGTGGCTGTGGAGGAACAAGACAGTGGTCACATACGTGGCCATGGC
CACCGAGGGCATGCTAGGGGCCTCCTATGTCGCGGTGCCCCTTTATAGGCTCTACTGCCAGAATACTGGACTTGGAGGAT
CAGCAGTGGCCGGGCACTCATCAGATCAGATTGAAAACAGGGTGCCTGTTAAGGATCGATCAGTAAAGTCACCTTTAATG
TCCGTTTCCAGTGGATCTTCAGACCTCAATGAACAGAGATCTATGTGGTACCAGTAGAGACTGCACTGGCATTTTATAAA
GCTAAAAATCCTACTCACAAACCAGTAATTGTAATTTCTACATATAATGTTGTACCGTTTGAAGCTGGCCAATATTTCAA
TAAAATACAGTGTTTCTGTTTTAAAGAACAAAGGCTTAATCCACAAGAAGAAGTGGATATGCCAGTGTTTTTCTACATTG
ACCCTGAATTTGCAGAAGATCTGAGAATGGCGAATGTCTATCCCATTACTCTTTCTTACCATTTTTTTTTTTTTGAAGCA
AAGGAAGGGCACAAGTTTCCAGTTCCAAGCTATAAT

Alignment

ORF - retro_mmus_2714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGLWCPGWRLVASCGRGWRQPGWSGRTVVNAELVLR-PGWDGLGGAERGLRRLGTWKR--PCGVRGPAT
          MGGLWCP.WR.V..CG..W.QP.WSGR...N.EL.LR.PGW..LGG.E.GLR.LGTWKR...C.......
Retrocopy MGGLWCPDWRFVTLCGQRWNQP*WSGRIGMNSELILRPPGWKELGGVEPGLRCLGTWKRLSECSPESHSL

Parental  QPPRRPR---SSNPFQRAQEDEWRRRNKTVLTYVAAAAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHS
          .P....R...SSNPFQ..QED.W..RNKTV.TYVA.A..GMLGASY.AVPLYRLYCQ.TGLGGSAVAGHS
Retrocopy PPAQPSR*LRSSNPFQCSQEDKWLWRNKTVVTYVAMATEGMLGASYVAVPLYRLYCQNTGLGGSAVAGHS

Parental  SDQIENMVPVKDR-VIKVTFNADVHASLQWNFRPQQTEIYVVPGETALAFYKAKNPTDKPVIGISTYNVV
          SDQIEN.VPVKDR...KVTFN.......QW.FRPQ.TEIYVVP.ETALAFYKAKNPT.KPVI.ISTYNVV
Retrocopy SDQIENRVPVKDR<ISKVTFN----VRFQWIFRPQ*TEIYVVPVETALAFYKAKNPTHKPVIVISTYNVV

Parental  PFEAGQYFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFAEDPRMVNVDLITLSY--TFFEAKEGHKLPV
          PFEAGQYFNKIQCFCF.EQRLNPQEEVDMPVFFYIDPEFAED.RM.NV..ITLSY.....EAKEGHK.PV
Retrocopy PFEAGQYFNKIQCFCFKEQRLNPQEEVDMPVFFYIDPEFAEDLRMANVYPITLSYXXXXXEAKEGHKFPV

Parental  PGYN
          P.YN
Retrocopy PSYN

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	0.00 RPM	6.79 RPM
SRP007412_kidney	0.02 RPM	5.06 RPM
SRP007412_liver	0.00 RPM	3.14 RPM
SRP007412_testis	0.00 RPM	4.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2714 was not detected

EST

No EST(s) were mapped for retro_mmus_2714 retrocopy.

TSS

No TSS is located nearby retro_mmus_2714 retrocopy 5' end.

Lab

retro_mmus_2714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2714 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,