Sequence
atgc intronic sequence ATGC exonic sequence...atattcctatttctgccatgatacttggtgattgctactgctgggacttgaaagtatattgatggtctttttttttctggtgttggtccttcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g42870.1 (Oryza sativa), 3'ss of exon 2
----atattcctatttctgccatg-atacttggtgattgctactgctgggacttgaaagtatattgatggtctttttttttctggtgttggtccttcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
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tggtaaatattcaatccagttagatatcactagagtgtactactactagcagcgcattgattagaagtggtggcacacac-ctgctgtttgttctggc----cagGTGGTCCATGATCGCGGCGCAGCTGCCCGGCCGGACCGACAACGAGATCAAGAACTATTGGAACACTCACCTCAAGAAGCAGCTGCGCCGGATGGGCCTC
upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 2
atattcctatttctgccatgatacttggtgattgctactgctgggacttgaaagtatattgatggtctttttttttctggtgttggtccttctt-cctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC--
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-ggaccctgttgatgcagtcccatcctcctatatttcgaggtcaatatggaccttccgcattttttgttttcatatgtgaactgaatgtaagatatttcagGTGGGCTGCAATCGCTTCAAAAATACCTGGTAGAACGGACAATGAGATCAAGAACTTCTGGAACACCCATCTAAAGAAGCGCCTCC--TGGGCAACCACCAA
upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S389_40V6.1 (Physcomitrella patens), 3'ss of exon 1
-atattcctatttctgccatgatacttggtgat-tgctactgctgggacttgaaagtatattgatggtctttttttttctggtgttggtccttcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
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tttgttttgttttgtttttttgtgtttttttgtgtgtgtgtgcgagtgcgtgga-gcacagaaaaattgattttttggaatgtgttg-ttgttgattcgcagATGGTCTGCCATAGCTAGCCATCTTCCTCGCCGCACTGACAACGAGATCAAGAACTACTGGAACACACACTTGAAGAAGCGTCTCATGCAAATGGGAATT
upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S106_216V6.1 (Physcomitrella patens), 3'ss of exon 2
-------atattcctatttctgccatg--atacttggtgattgctactgctgggacttgaaagtatattgatggtctttttttttctggtgttggtccttcttcctc---------agGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
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gtactgaattttcttcccgtcgcgttgggatgtctcatttctgcagacgtcgcgcgttggttacactccacaaaattgtcagttcctaacagcatttctcgtttcttgattgcattagATGGTCAGCCATCGCGGGCCATCTCCCCCAGCGTACAGACAACGAGATAAAGAACTACTGGAACACGCATTTGAAGAAACGTTTGGCACAGATGGGAATC
upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 2
---atattcctatttctgccatgatacttggtgattgctactgctgggacttgaaagtatattgatg-gtctttttttttctggtgttggtccttcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
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ttgaaattttacttctttttgtaacagttaggactagttatcttgaatacc----atttttttaatatatcgctttcttatttatttatttatttatattgtagGTGGTCAGCCATAGCAAGCCATCTTCCCCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACGCACTTGAGGAAGCGACTGCTGCAAATGGGGATT
upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ18722 (Selaginella moellendorffii), 3'ss of exon 1
atattcctatttctgccatgatacttggtgattgctactgctgggacttgaaagtatattgatggtctttttttttctggtgttggtccttcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
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-----------------gtgaaacc-ggtaacagtt--tgtagagttttacctctaaattctgcgttctctaagttcttgcgt----gtttcactttcagGTTGTCCGTGATCGCATCGCACATTCCTGGACGAATTGACAACGAGATTAAAAACCACTGGAACACACACCTCAAGAAG---------------------
upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ18565 (Selaginella moellendorffii), 3'ss of exon 1
atattcctatttctgccatgatacttggtgattgctactgctgggacttgaaagtatattgatggtctttttttttctggtgttggtccttcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
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---------------------------gtaacagtt--tgtagagttttacctctaaattc-ttgcgttctctaagctcttgc--gtgtttcactttcagGTGGTCCGTGATCGCATCGCACATTCCTGGACGAACTGACAACAAGATTAAAAACTACTGGAACACACACCTCAAGAAGCAATTGTTGCAAATGGGAATC
upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ18723 (Selaginella moellendorffii), 3'ss of exon 2
atattcctatttctgccatgatacttggtgattgctactgctgggacttgaaagtatattgatggtctttttttttctggtgttg-gtccttcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
| ||| | ||| | ||| | | | | ||| || || ||||||||||| ||||||| |||| | ||||| || || ||||||||||| || ||| |||||||||| |||||||||||||| || | |||||| |
-------------------------------------------------gtaagagt-ttgtagagttttacctctaagttcttgcgtttctcactttcagGTGGTCCGTGATCGCATCGCACATTCCTGGACGAACTGACAACGAGATTAAAAACCACTGGAACACACACCTCAAGAAGCAATTGTTACAGATGGGGATTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|91874168|gb|EB404125.1|EB404125EST: TCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAA GTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAA
genomic: TCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAAgtaagcccag ... tcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAA
EST:
gi|76285013|gb|DV024581.1|DV024581EST: TCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAA GTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAA
genomic: TCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAAgtaagcccag ... tcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAA
EST:
gi|71308073|gb|DR790252.1|DR790252EST: TCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAA GTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAA
genomic: TCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAAgtaagcccag ... tcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAA
EST:
gi|91048016|gb|EB158434.1|EB158434EST: TCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAA GTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGG
genomic: TCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAAgtaagcccag ... tcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 2 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
24TGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAAgtaagcccag ... tcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
Block sizes:
49 (upstream exon),
9 (downstream exon)
Score:
2TGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCATCGTCCAGCTCCACGCCATCGTCGGCAACAAgtaagcccag ... tcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgaaagtatattgatggtctttttttttctggtgttggtccttcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
tattgat putative branch site (score: 2)
ttggtccttcttcctc putative PPT
tcttttttttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattcctatttctgccatgatacttggtgattgctactgctgggacttgaaagtatattgatggtctttttttttctggtgttggtccttcttcctcagGTGGTCCATGATCGCGGCGCAGCTCCCTGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCAGCTGCGTCGGATGGGCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - ttctgcc
- - - - - - - - - tgatact
- - - - - - - - - - - - - - tgattgc
- - - - - - - - - - - - - - - - - - actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggt