RetrogeneDB ID: retro_mmus_11

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:16768269..16770138(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000091020
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Tox4
• Ensembl ID: ENSMUSG00000016831
• Aliases: Tox4, 5730589K01Rik, A630040M18, AA410149, LCP1
• Description: TOX high mobility group box family member 4 [Source:MGI Symbol;Acc:MGI:1915389]

Sequence

>retro_mmus_11
ATGGAGTTTCCCAGAGGAAATGACAATTACCTGACAATCACTGGGCCCTCGCACCCTTTCCTGTCAGGGGCCGAGACATT
ACATACACCAAGCTTGGGCGATGAGGAATTTGAAATTCCACCTATCTCCTTGGACTCTGATCCCTCACTGGCTGTCTCAG
ATGTGGTTGGCCACTTTGATGACCTGGCAGACCACTCCTCTTCACAGGATAGCAGCTTTTCAGCTCAGTACGGGGTCCAG
ACATTGGACATGCCTGTGGGCATGACCCATGGCTTGATGGAGCAGGGCGGGGGGCTCCTGAGTGGGGGCTTGACTATGGA
CCTGGACCATTCTATAGGAACTCAGTATAATGCCAACCCACCTGCTACAATTGATGTACCAATGACAGACATGACATCTG
GCTTAATGGGACACAGCCAGTTGACCTCTATTGGTCAGTCAGAACTGAGTTCTCAACTTGGTTTGAGTTTAGGAGGTGGC
ACTATCTTGCCACCTGCCCAGTCACCTGAGGATCGTCTTTCAACTACTCCTTCACCTACCAGTTCACTTCATGAGGATGG
GGTTGATGATTTCCGGAGGCAACTTCCCGCCCAGAAGATAGTGGTAGTGGAAACAGGGAAAAAGCAAAAGGCTCCCAAGA
AGAGAAAAAAGAAAGACCCAAATGAACCGCAGAAGCCAGTCTCTGCTTATGCATTGCTCTTTCGAGATACACAGGCTGCC
ATCAAGGGACAAAACCCGAATGCAACCTTTGGGGAGGTATCGAAGATTGTGGCTTCCATGTGGGACAGTCTTGGAGAAGA
ACAGAAGCAGGTGTACAAGCGGAAGGCTGAGGCTGCCAAGAAAGAGTATCTCAAGGCACTAGCTGCTTATAAAGACAACC
AGGAATGCCAGGCTACTGTGGAAACCGTGGAATTAGATCCTGTGCCACAGTCACAGACTCCTTCCCCACCTCCTGTGACT
ACTGCTGACCCAGCATCTCCAGCACCAGCCTCAACGGAGTCTCCTGCTTTGCCCCCTTGCATCATAGTGAATTCCATGCT
TTCATCTAATGTGGCAAACCAAGCCTCTTCTGGGCCTGGAGGTCAGCCCAATATTACCAAGTTGATTATTACCAAACAGA
TGTTGCCTTCTTCTATCACCATGTCCCAAGGAGGAATGGTTACTGTTATCCCAGGCACAGTGGTTACCTCCCGTGGTCTC
CAGGTAGGCCAAACAAGTACAGCTACTATTCAGCCAAGCCAGCAGGCCCAGATTGTCACCCGGTCAGTGTTGCAGGCAGC
AGCAGCTGCTGCTGCTTCCATGCAACTGCCTCCACCCCGACTACAGCCCCCTCCGTTGCAGCCCCCTCCGTTGCAACAGA
TGCCTAAGCCCCCAATTCAACAGCAAATCACCATTCTACAGCAACCCCCTCCACTTCAGGCCATGCAGCAACCTCCACCT
CAGAAAGTTAGAATCAACTTACAGCAGCAGCCACCTCCTCTGCAGAGCAAGATTGTGCCTCCACCCACTCTGAAAATACA
GACTACTGTGGTCCTTCCAACTGTAGAAAGCAGTCCTGAGCAGCCTATGAACAGCAGCCCCGAGGCCCACACAGTAGAGG
CAACCTCTCCTGAGACAATCTGTGAAATGATCGAAGTAGTTCCTGAGGTGGAGTCTCCTTCTCAGATGAATGTTGAATTG
GTGAGTGGCTCCCCTGTGACACTGTCACCTCAGCCTGGATGTGTGAGGTCTAGTTGTGAGAACCCTCCTGTTATCAGTAA
GGACTGGGACAACGAGTACTGCAACAATGAGTGTGTGGTGAAGCACTGCAGGGATGTATTCTTGGCCTGGGTGGCCTCTA
GAAATCCAAACTCTGGTGTTTGTGAGGTA

Alignment

ORF - retro_mmus_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.56 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEFPGGNDNYLTITGPSHPFLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVVGHFDDLADPSSSQD
          MEFP.GNDNYLTITGPSHPFLSGAET.HTPSLGDEEFEIPPISLDSDPSLAVSDVVGHFDDLAD.SSSQD
Retrocopy MEFPRGNDNYLTITGPSHPFLSGAETLHTPSLGDEEFEIPPISLDSDPSLAVSDVVGHFDDLADHSSSQD

Parental  GSFSAQYGVQTLDMPVGMTHGLMEQGGGLLSGGLTMDLDHSIGTQYSANPPVTIDVPMTDMTSGLMGHSQ
          .SFSAQYGVQTLDMPVGMTHGLMEQGGGLLSGGLTMDLDHSIGTQY.ANPP.TIDVPMTDMTSGLMGHSQ
Retrocopy SSFSAQYGVQTLDMPVGMTHGLMEQGGGLLSGGLTMDLDHSIGTQYNANPPATIDVPMTDMTSGLMGHSQ

Parental  LTTIDQSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPTNSLHEDGVDDFRRQLPAQKTVVVETGKKQK
          LT.I.QSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPT.SLHEDGVDDFRRQLPAQK.VVVETGKKQK
Retrocopy LTSIGQSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPTSSLHEDGVDDFRRQLPAQKIVVVETGKKQK

Parental  APKKRKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKTEAAK
          APKKRKKKDPNEPQKPVSAYAL.FRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRK.EAAK
Retrocopy APKKRKKKDPNEPQKPVSAYALLFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAK

Parental  KEYLKALAAYKDNQECQATVETVELDPVPQSQTPSPPPVTAADPASPAPASTESPALPPCIIVNSTLSSY
          KEYLKALAAYKDNQECQATVETVELDPVPQSQTPSPPPVT.ADPASPAPASTESPALPPCIIVNS.LSS.
Retrocopy KEYLKALAAYKDNQECQATVETVELDPVPQSQTPSPPPVTTADPASPAPASTESPALPPCIIVNSMLSSN

Parental  VANQASSGPGGQPNITKLIITKQMLPSSITMSQGGMVTVIPATVVTSRGLQVGQTSTATIQPSQQAQIVT
          VANQASSGPGGQPNITKLIITKQMLPSSITMSQGGMVTVIP.TVVTSRGLQVGQTSTATIQPSQQAQIVT
Retrocopy VANQASSGPGGQPNITKLIITKQMLPSSITMSQGGMVTVIPGTVVTSRGLQVGQTSTATIQPSQQAQIVT

Parental  RSVLQAAA-AAAASM----QLPPPRLQPPPLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQQQ
          RSVLQAAA.AAA........L.PP.LQPPPLQQMP.PP.QQQ.TILQQPPPLQAMQQPPPQKVRINLQQQ
Retrocopy RSVLQAAAAAAASMQLPPPRLQPPPLQPPPLQQMPKPPIQQQITILQQPPPLQAMQQPPPQKVRINLQQQ

Parental  PPPLQSKIVPPPTLKIQTTVVPPTVESSPEQPMNSSPEAHTVEATSPETICEMIADVVPEVESPSQMDVE
          PPPLQSKIVPPPTLKIQTTVV.PTVESSPEQPMNSSPEAHTVEATSPETICEMI..VVPEVESPSQM.VE
Retrocopy PPPLQSKIVPPPTLKIQTTVVLPTVESSPEQPMNSSPEAHTVEATSPETICEMI-EVVPEVESPSQMNVE

Parental  LVSGSPVALSPQPRCVRSGCENPPVVSKDWDNEYCSNECVVKHCRDVFLAWVASRNPNSVV
          LVSGSPV.LSPQP.CVRS.CENPPV.SKDWDNEYC.NECVVKHCRDVFLAWVASRNPNS.V
Retrocopy LVSGSPVTLSPQPGCVRSSCENPPVISKDWDNEYCNNECVVKHCRDVFLAWVASRNPNSGV

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	0.09 RPM	60.21 RPM
SRP007412_cerebellum	1.65 RPM	62.53 RPM
SRP007412_heart	0.09 RPM	45.01 RPM
SRP007412_kidney	1.33 RPM	50.20 RPM
SRP007412_liver	0.33 RPM	32.63 RPM
SRP007412_testis	3.16 RPM	65.04 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_11 was not detected

EST

No EST(s) were mapped for retro_mmus_11 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_71379	164 libraries	290 libraries	581 libraries	29 libraries	8 libraries

The graphical summary, for retro_mmus_11 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_11 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_11 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006261	1 retrocopy	retro_amel_858,
Canis familiaris	ENSCAFG00000005647	2 retrocopies	retro_cfam_1625, retro_cfam_1698,
Choloepus hoffmanni	ENSCHOG00000000714	2 retrocopies	retro_chof_2239, retro_chof_631,
Homo sapiens	ENSG00000092203	1 retrocopy	retro_hsap_2970,
Macropus eugenii	ENSMEUG00000010501	1 retrocopy	retro_meug_1384,
Mustela putorius furo	ENSMPUG00000000181	1 retrocopy	retro_mputfur_718,
Mus musculus	ENSMUSG00000016831	1 retrocopy	retro_mmus_11 ,
Nomascus leucogenys	ENSNLEG00000014556	1 retrocopy	retro_nleu_2027,
Pongo abelii	ENSPPYG00000005598	1 retrocopy	retro_pabe_2463,
Pan troglodytes	ENSPTRG00000006126	1 retrocopy	retro_ptro_2008,
Sus scrofa	ENSSSCG00000029203	1 retrocopy	retro_sscr_361,