RetrogeneDB ID: retro_mmus_315

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:45971187..45972595(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mier3
• Ensembl ID: ENSMUSG00000032727
• Aliases: Mier3, 5730509D14, AU015422, D130064H19Rik
• Description: mesoderm induction early response 1, family member 3 [Source:MGI Symbol;Acc:MGI:2442317]

Sequence

>retro_mmus_315
TTGTCTTCTGAGGATCATGATGTTGACCCCACTGCTTAGATGTTGGCCCATGACTATGATGATGAAAGAACTATAGAGGA
AGAGAAATTGATGGATTACAGGGAAAACTTCAGTTCTGAAATTGAAGAGTTAGAAAAGGAAGGAAATATGCCTCTAGAAG
ACCTATTGGCATTCCACAGCTATGAATCTACACTTCAAACAGTTTCAAATTCTAGTGCAAACAGCTCCCCAAGTGAACTT
GCAGAAGAACTACCAGATATGACTCTAGGCAAAGAAAAACAGCGAAAGACCTGTTGTTAGGCGATGATGAGGAAATTCAG
TCTTCTGCAGATGATCTGATACCATCTGTGACTTCTCATGAAACTTCTGCTTTCTTCCCTCTGCCTTTATGATCAAACGC
TGCATGTGATGGAAACAAGGAATCAGAGACTTAGGACGTTGAAATGGACAGTGGTAACTAACCTGAAGATTTGAAAAGGG
AAATAATGATTGGTCTACAGTATCAGGCAGAAATTCCCCCTTATCTTGGCGAGTACAATGGTGATGAGAAAGCTTATGAA
AATGAAGACCAGTTACTGCGGGCATCCTGATGTGGTTTGTAGAACAAAGTCAAGGACTTTATTGAGACCTCATTAAGAAC
TAGAAATGAAAAAGCCCTAGACAGAATTTTTTCAGGCACACACACCAGGGATAATGAACAGGCAATATATGAACTTCTCA
AGTGTAACCACAAAATAAAGGAAGCAATTGAAAGGAACTGCTGTAATGGAAAGGCATCTCCAGAAGGAATGACAGCATGG
ACTGAAGAGGAGTGCTGAAGCTTTGAACACGAACTAATGTTTTACGGAAAAGATTTTTATCTCATTCAGAAAGATAAGGT
GAGATCTAGAACTGTTGCCAAGTGTATAGCCTTCCACTACATGTGGAAGAAATCGAATGCTATGATTACTTTGCTCAACA
GACAATGTTTGGAAAGAAATTCTATAACCATCACCCTGGCATTACGGACTATAGGGATCATCTCATAGATGAAACAGAGT
CTCTGGGTGGTACGATCAGTTCTTCAGCTTTAACTTCTAACTGGCAGGACCCCATTCCTTATCAGCTGCTGAACATTCTT
AGCTCCTTCACTGCCAGAGACTTGAGAGCTTTGACCAACAGTGTAGCAACTGTCTGCACCCCCACAGCTGTGAATTGTCT
GGATGATAACTTTCCTCCACTGGGAAAAACGCCTCGTGGACAAGTCAATCATGTGCCTGTCGTAACGGAAGAGTTACTCA
CCCTGCCCAGCAATGGTGAAAGTGATTGTTTTAATTTATTTGAGACTGGATTTTGTCACTCAGAATTAAACCCCATGTGC
AGCGAAGAATCAGAAAGACCAGCAAAGAGATTGAAAATGGGCATTGCA

Alignment

ORF - retro_mmus_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 85.66 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSSEDHDFDPTAEMLVHDYDDERTLEEEELMDDGKNFSSEIEDLEKEGNMPLEDLLAFYGYESTIPAVAN
          LSSEDHD.DPTA.ML.HDYDDERT.EEE.LMD...NFSSEIE.LEKEGNMPLEDLLAF..YEST...V.N
Retrocopy LSSEDHDVDPTA*MLAHDYDDERTIEEEKLMDYRENFSSEIEELEKEGNMPLEDLLAFHSYESTLQTVSN

Parental  SSANSSPSELADELPDMTLDKEE-IAKDLLSGDDEETQSSADDLTPSVTSHETSEFFPRPLRSNTTCDGD
          SSANSSPSELA.ELPDMTL.KE...AKDLL.GDDEE.QSSADDL.PSVTSHETS.FFP.PL.SN..CDG.
Retrocopy SSANSSPSELAEELPDMTLGKEK<TAKDLLLGDDEEIQSSADDLIPSVTSHETSAFFPLPL*SNAACDGN

Parental  KESEIEDVETDSGNSPEDLRREIMIGLEYQAEIPPYLGEYNGDDEKAYENEDQLL-WHPGVL-LESKVKE
          KESE..DVE.DSGN.PEDL.REIMIGL.YQAEIPPYLGEYNGD.EKAYENEDQLL..HP.V..L..KVK.
Retrocopy KESET*DVEMDSGN*PEDLKREIMIGLQYQAEIPPYLGEYNGD-EKAYENEDQLL>GHPDVV<L*NKVKD

Parental  YLVETSLRTGNEKVLDRISSGTHTRDNEQALYELLKCNHNIKEAIERYCCNGKASQEGMTAWTEEECRSF
          ...ETSLRT.NEK.LDRI.SGTHTRDNEQA.YELLKCNH.IKEAIER.CCNGKAS.EGMTAWTEEEC.SF
Retrocopy F-IETSLRTRNEKALDRIFSGTHTRDNEQAIYELLKCNHKIKEAIERNCCNGKASPEGMTAWTEEEC*SF

Parental  EHALMLHGKDFHLIQKDKVRSRTVAECVAFYYMWKKS-ERYDYFAQQTKFGKKRYNHHPGVTDYMDRLVD
          EH.LM..GKDF.LIQKDKVRSRTVA.C.AF.YMWKKS.E.YDYFAQQT.FGKK.YNHHPG.TDY.D.L.D
Retrocopy EHELMFYGKDFYLIQKDKVRSRTVAKCIAFHYMWKKS<ECYDYFAQQTMFGKKFYNHHPGITDYRDHLID

Parental  ETESLGGTVSSSALTCNRPEPVPDQPLNILSSFTASDLTALTNSVATVCNPTAVNCLDDSFPPLANTPRG
          ETESLGGT.SSSALT.N...P.P.Q.LNILSSFTA.DL.ALTNSVATVC.PTAVNCLDD.FPPL..TPRG
Retrocopy ETESLGGTISSSALTSNWQDPIPYQLLNILSSFTARDLRALTNSVATVCTPTAVNCLDDNFPPLGKTPRG

Parental  HVNHVPVVTEELLTLPSNGESDCFNLFETGFYHSELNPMCSEESERPAKRLKMGIA
          .VNHVPVVTEELLTLPSNGESDCFNLFETGF.HSELNPMCSEESERPAKRLKMGIA
Retrocopy QVNHVPVVTEELLTLPSNGESDCFNLFETGFCHSELNPMCSEESERPAKRLKMGIA

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	23.48 RPM
SRP007412_cerebellum	0.00 RPM	27.70 RPM
SRP007412_heart	0.00 RPM	12.98 RPM
SRP007412_kidney	0.00 RPM	23.00 RPM
SRP007412_liver	0.00 RPM	17.64 RPM
SRP007412_testis	0.00 RPM	110.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_315 was not detected

EST

No EST(s) were mapped for retro_mmus_315 retrocopy.

TSS

No TSS is located nearby retro_mmus_315 retrocopy 5' end.

Lab

retro_mmus_315 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_315 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000000655	2 retrocopies	retro_mluc_2537, retro_mluc_437,
Mus musculus	ENSMUSG00000032727	1 retrocopy	retro_mmus_315 ,