RetrogeneDB ID: retro_mmus_1144

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:108309659..108310825(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Net1
• Ensembl ID: ENSMUSG00000021215
• Aliases: Net1, Net1a, mNET1
• Description: neuroepithelial cell transforming gene 1 [Source:MGI Symbol;Acc:MGI:1927138]

Sequence

>retro_mmus_1144
ATGGTGGCGCATGAGATCGGAGGTCTCCTGCCCATTAAAAGGACAATCCGAGTTTTAGATGTTAATAACCAGCCCTCCCG
GGAGCAGGAGGAGCCAAGCCATAAGAGAGTTTGGCCTCTAGCTCAGGTCACATCCTTGGCAAACTTAATCTCTCCCATAA
GAAATGGAGCAGTCAGGCGCTTCGGTCAGACCATACAGTCGTTTACCCTTCGTGGTGACCACAGATCCCCAGCCTCTGCC
CAGAAGACATTCAGCAGGTCCACCGTCCCCACACCCACCAAGAGAAGAAGCAGTGCACTATGGTTGGAAATGCTAGACAT
CAATATGAAGGAGCCCTTGACCACTCGAGAGATCAAACGTCAGGAGGCTATATATGAATTGTCCCGAGGAGAACAGGACT
TGATTGAGGATCTCAAGCTCGCTAGAAAGGCCTACCATGACCCCATGTTAAAGCTGTCCATCATGTCAGAAGAGGAACTC
ATGCACATATTTGGAGACTTGTATGCTTACATACCTCTGCACGAAGATCTGTTAGCAAGAATTGGAGAAGCAACCAAGCC
TGATGGGTCTGTGGAGCAGATCGGTCACATTCTCGTGAACTGGTTACCAGGCCTGAATGCCTACAGAGGCTACTGTAGTA
ACCAGCTGGCGGCCAAGGCTCTTCTGGATCAGAAGAAACAAGATCCAAGAGTCCAAGACTTCCTCAGCGCTGTCTGGAGT
CCCCTTTCAGTCGAAAACTAGATCTTTGGAGTTTCCTAGATATCCCTTGAAGTCGCCTCGTCAAGTACCCCTTACTGTTA
AAAGAAAGCCTTAGACACACTCCCAAAGACCACCATGATGTTCAGCTTCTGGAGGAGGCAATATTGATAATACAAGGAGT
TCTTTCTGATATCAACTTGAAGAAAGGCGAATCTGAGTGTCAGTATTACATCAACAAGCTGGAGTACCTGGACGAGAAGC
AGAAGGACCCTAGGATCGAAGCGAGCAAAGTGCTGCTGTGCCATGGGGAGCTGAAGAATAAAAGCGGCCATAAACTGTAC
ATTTTCCTATTTCAAGACATCTTGGTTTCGACTCGGCCTGTCACCCGAAATGAGCGCCACTTGTACCAGGTTTACTGGCA
GCCCATCCCAGTCCAGGAGCTGGTGCTGGAAGACCTACCTGCAGGA

Alignment

ORF - retro_mmus_1144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.88 %
• Parental protein coverage: 72.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVAHDEIGGLLPIKRTIRVLDVNNQPFREQEEPSNKRVRPLARVTSLANLISPVRNGAVRRFGQTIQSFT
          MVAH.EIGGLLPIKRTIRVLDVNNQP.REQEEPS.KRV.PLA.VTSLANLISP.RNGAVRRFGQTIQSFT
Retrocopy MVAH-EIGGLLPIKRTIRVLDVNNQPSREQEEPSHKRVWPLAQVTSLANLISPIRNGAVRRFGQTIQSFT

Parental  LRGDHRSPASAQKSFSRSTVPTPTKRRSSALWSEMLDINMKESLTTREIKRQEAIYELSRGEQDLIEDLK
          LRGDHRSPASAQK.FSRSTVPTPTKRRSSALW.EMLDINMKE.LTTREIKRQEAIYELSRGEQDLIEDLK
Retrocopy LRGDHRSPASAQKTFSRSTVPTPTKRRSSALWLEMLDINMKEPLTTREIKRQEAIYELSRGEQDLIEDLK

Parental  LARKAYHDPMLKLSIMSEEELTHIFGDLDAYIPLHEDLLARIGEATKPDGTVEQIGHILVNWLPGLNAYR
          LARKAYHDPMLKLSIMSEEEL.HIFGDL.AYIPLHEDLLARIGEATKPDG.VEQIGHILVNWLPGLNAYR
Retrocopy LARKAYHDPMLKLSIMSEEELMHIFGDLYAYIPLHEDLLARIGEATKPDGSVEQIGHILVNWLPGLNAYR

Parental  GYCSNQLAAKALLDQKKQDPRVQDFL-QRCLESPFSRKLDLWSFLDIPRSRLVKYPLLLKEILRHTPKDH
          GYCSNQLAAKALLDQKKQDPRVQDFL.QRCLESPFSRKLDLWSFLDIP.SRLVKYPLLLKE.LRHTPKDH
Retrocopy GYCSNQLAAKALLDQKKQDPRVQDFL<QRCLESPFSRKLDLWSFLDIP*SRLVKYPLLLKESLRHTPKDH

Parental  RDVQLLEEAILIIQGVLSDINLKKGESECQYYINKLEYLDEKQKDPRIEASKVLLCHGELKNKSGHKLYI
          .DVQLLEEAILIIQGVLSDINLKKGESECQYYINKLEYLDEKQKDPRIEASKVLLCHGELKNKSGHKLYI
Retrocopy HDVQLLEEAILIIQGVLSDINLKKGESECQYYINKLEYLDEKQKDPRIEASKVLLCHGELKNKSGHKLYI

Parental  FLFQDILVLTRPVTRNERHLYQVYRQPIPVQELVLEDLQDG
          FLFQDILV.TRPVTRNERHLYQVY.QPIPVQELVLEDL..G
Retrocopy FLFQDILVSTRPVTRNERHLYQVYWQPIPVQELVLEDLPAG

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	25.12 RPM
SRP007412_cerebellum	0.00 RPM	16.11 RPM
SRP007412_heart	0.03 RPM	12.39 RPM
SRP007412_kidney	0.13 RPM	86.49 RPM
SRP007412_liver	0.11 RPM	38.50 RPM
SRP007412_testis	0.09 RPM	21.18 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1144 was not detected

EST

No EST(s) were mapped for retro_mmus_1144 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_26475	405 libraries	288 libraries	321 libraries	36 libraries	22 libraries

The graphical summary, for retro_mmus_1144 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010007	1 retrocopy	retro_chof_1896,
Monodelphis domestica	ENSMODG00000018500	2 retrocopies	retro_mdom_21, retro_mdom_239,
Mus musculus	ENSMUSG00000021215	1 retrocopy	retro_mmus_1144 ,