RetrogeneDB ID: retro_mmus_1865

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:28974575..28975604(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tekt5
• Ensembl ID: ENSMUSG00000039179
• Aliases: Tekt5, 3300001K11Rik
• Description: tektin 5 [Source:MGI Symbol;Acc:MGI:1917676]

Sequence

>retro_mmus_1865
ATGGAATTTCTTGGAACCATTCAGACAGCGAGTTACTGTGGCTCCAAGAAAGACTGTGGCTTGCAGTGGCCGCCCCCTGC
TGGGCAGGACCCTGAGGTACAGGAGTGCTACCAATCCTTTCACCTGCCCCGCTGCCGCTCTGCTTGGAGACCCAGAGTCT
TCTACAAGGTCGCCACCACCCAGAAAAGCCAGGAGGATAGCGCAGGCGACCAGGGGCTGTCCACAATTCTGCCCTCGCTC
CACTCCCCGCACTTCAATCGTTATACCCAACGCGAATGGGACCGCTCTAATGATCTGCTGATCAGTATTGCAGAGGCATC
GCGGCTCCGCGCCAGCCGGCTGACAGACGACTCCCTGCGGATCATGCAGGATAAGGAGCAGCTGACACGCCAGATGCAAG
AGGGAACCTTCCGGAACCTGGGCCAGAGGCTCTCCGACATCCGCTTCTGGAAGTCCGGGTTGTGTCATGAGCGGGACATG
CTGATGGCGGAGATCAACAACTTGAAAACCCTCAAGATGCGCTTGGAGTGCGCCGCTAAGGAGGTGAACTGTCCCCTGCA
GGTGACCCTGGACTATCTGTACAGTAAGGAGAAAAGGATCGGGATTAACCTGGTCCATGACAACGGGGAGAAAAACCTTC
TCCGGGTAGCAGATTTACTTAAATGTTGCCAAGATCAGATGAGAAAATTAGCTAAACGAATTGATTCCCAGATGCAAGAT
AATCGAGATGTTCAACATGCCCTAGAGCAAGACATCGCAGACAAGAGCTCTGCACAGTCTATTGAGGAGAGATGTTTAAA
CCTAAAAAACACATCTGAATCCATTAACTTCTTCCGTGGCATGGAGAACTTTGACGAAACGGTCTCCGTTCCTGAAACCT
GGGCCAAGTTCAGCAGTAACAACATCAGACACGCTCAGACTACGCGGGCCAAGTCTGTCCAGCTGCGGGAGGAGGTAGAG
CACCTGTTTGAGACCTTGACAGCCCAGGTGTGGAGGCATTTCACCAACATCAACCTGGCCTACCAGTCT

Alignment

ORF - retro_mmus_1865 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.28 %
• Parental protein coverage: 83.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEFLGTTQTASFCGPKKGCGLQALPPAGQEPVVQECYQPFHLPGYRYLNAWRPSVFHKIATSQTIPEECS
          MEFLGT.QTAS.CG.KK.CGLQ..PPAGQ.P.VQECYQ.FHLP..R...AWRP.VF.K.AT.Q...E...
Retrocopy MEFLGTIQTASYCGSKKDCGLQWPPPAGQDPEVQECYQSFHLPRCR--SAWRPRVFYKVATTQKSQEDSA

Parental  GIRRPPTILPSLRSALFCRYTPRDWDRSNDLQIRNAEASRLWASRLTGDSLRIMQDKDQLIHQMQEGTSR
          G.....TILPSL.S..F.RYT.R.WDRSNDL.I..AEASRL.ASRLT.DSLRIMQDK.QL..QMQEGT.R
Retrocopy GDQGLSTILPSLHSPHFNRYTQREWDRSNDLLISIAEASRLRASRLTDDSLRIMQDKEQLTRQMQEGTFR

Parental  NLGQRLSDLGFWKSELCYELDRLLTENSSMDTLKRRLECAAEEVNCPLQVALECLYNREKRIGIDLVHDN
          NLGQRLSD..FWKS.LC.E.D.L..E.....TLK.RLECAA.EVNCPLQV.L..LY..EKRIGI.LVHDN
Retrocopy NLGQRLSDIRFWKSGLCHERDMLMAEINNLKTLKMRLECAAKEVNCPLQVTLDYLYSKEKRIGINLVHDN

Parental  VEKNLIREVDLLKCCQDQMRKLAKRIDFQIRDNRDAQHSLERDIEDKSSAQYIDENCFNLRSTSDSISFF
          .EKNL.R..DLLKCCQDQMRKLAKRID.Q..DNRD.QH.LE.DI.DKSSAQ.I.E.C.NL..TS.SI.FF
Retrocopy GEKNLLRVADLLKCCQDQMRKLAKRIDSQMQDNRDVQHALEQDIADKSSAQSIEERCLNLKNTSESINFF

Parental  HGVEKFDGTVSIPETWAKFSNDNIRHAQNMRANSIRLREEAEHLFETLSDQMWKQFTNTNLAFNA
          .G.E.FD.TVS.PETWAKFS..NIRHAQ..RA.S..LREE.EHLFETL..Q.W..FTN.NLA...
Retrocopy RGMENFDETVSVPETWAKFSSNNIRHAQTTRAKSVQLREEVEHLFETLTAQVWRHFTNINLAYQS

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	0.14 RPM	7.78 RPM
SRP007412_cerebellum	0.04 RPM	6.86 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.04 RPM	0.31 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	15.41 RPM	141.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1865 was not detected

EST

No EST(s) were mapped for retro_mmus_1865 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_63407	1067 libraries	2 libraries	1 library	0 libraries	2 libraries
TSS #2	TSS_63408	1067 libraries	2 libraries	1 library	0 libraries	2 libraries

The graphical summary, for retro_mmus_1865 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_1865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1865 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_654

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000039179	1 retrocopy	retro_mmus_1865 ,
Rattus norvegicus	ENSRNOG00000002571	1 retrocopy	retro_rnor_654,