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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA

Basic information

species Zea mays
transcript GRMZM2G128771_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------nnnnnnnnnnnnnnnnnnncacattactatttgagttttggta---gctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
                                                                      | ||||   ||    || |  |    ||  | ||  ||    ||||| |         ||  | || |  ||     |  ||||||||||||||| || || |||||||| ||||| |||||||||||||| || || ||||||||||| ||  |||| ||||||||| |||
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA

upper sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------nnnnnnnnnnnnnnnnnnncacattactatttgagtt-ttggta-gctttgttagttcattttcttggagaacagttagcatttcat-tgttcttgctgt-cagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
                                                                       | ||||   |     ||  ||||| || || |  |  |  ||| ||     |   |  |   ||  | | |  |  ||   ||||||||||||||| || || || ||||| ||||| |||||||||||||| || || ||||||||||||||  | || ||||||||  | |
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA

upper sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
------------------------------------------------nnnnnnnnnnnnnnnnnnncacattac-tatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
                                                                    | ||| |  |||   || | || |  ||| |||   |||| | ||| |    |   |   ||||||  ||     |  ||||||||||||||| || || || ||||| ||||| |||||||||||||| || || ||||||||||| || ||||| || |||||| |||
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattct-ttgtatgttaaa-attgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA

upper sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------nnnnnnnnnnnnnnnnnnncacattactatttgagtt-ttggta-gctttgttagt-tcattttcttggagaacagttagcatttcattgttcttgctgt-cagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
                                                                           | ||||   |     ||  ||||| || | ||  |  |  |||  ||  | ||    |    ||    | |  |  ||   ||||||||||||||| || || || ||||| ||||| |||||||||||||| || || ||||||||||| ||  | || ||||||||  | |
gtaggatgaattcctcttcaaatcatatatacaagctcagtctttttatatttgtttgtttatttttcaacaattatattagagtgcacattgctggtatgcctagtaggcattgtttatttttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATAGTATATGATGTTGCTA

upper sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
                     | |   ||  | |    |   |    ||||| ||        |  | | || | | ||   ||  ||| |   ||  ||||||||||| ||||| || || || |||||||| || ||||| |||||||| || |||||||||||  | ||||| || ||||||||||
gtgagaacaatgttacttttgc-tctttacctaaaaactaaca----tgttaatt--------tcaaaagcaat-aacaaaacaa-gttttgattgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA

upper sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgtta-gttcattttcttggagaacagttagcatttcattgttcttgctgt-cagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
                     |||    |||       | ||   |     | ||||||| | || |  |   || |   ||| | |  | || |||| |||||||||||||||||||||||| ||| | ||||| || ||||| || ||||| || ||||||||||| ||  |||| ||||||||  | |
tgaatggaacatcaaaatgtccatggaaattctcagcattgtgtatcaaccatgttcattcttttagttatatgtcat--tttgaatcatattactgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA

upper sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA-----------
                   |          | | | ||   | ||  ||| |    |||  |   ||| | || ||  | |      || | | | | |||||||| || ||||| || || || |||||| | || ||||| ||||| || || ||||||||||| || ||||||||||||||| |||           
gtaagaaatgctgttttttc----------tagggcttc--tcgcaatgtaa---tattcgcaatgagga-agctaataatgtga-attttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA

upper sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
-nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
                     |  ||   ||        |  | |  || || ||| || | |||  ||     | |   |||   | ||     |  |||||||||||| || || || || |||||||||||||| ||||||||||| || || ||||| ||||| ||| |||||||||||||    |
gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagt-ttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA

upper sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S39_147V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------nnnnnnnnnnnnnnnnnnncacattactatttgagttt--tggtagctttg--tta-gttcattttcttggaga-----acagttagcatttca----ttgttcttgctgt-cagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
                                                                                       |  || || ||||  |||  ||   |||||   |||     ||    || || |      |  ||    | |||    |||  | || ||  |||||| ||||| ||||||||||||||||||||| | ||||| ||||||||| |||| || || || || |||||||| |||||||| ||||
gtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA

Mapped 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|149095335|gb|EE180972.2|EE180972
EST:     CTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTG                         GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAG
genomic: CTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTGgtaagtatca ... ttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAG
EST: gi|211449139|gb|FL349634.1|FL349634
EST:     TGTCAAAAACAATGTATCTAGGAAGACCGAACTGTACGTTTACAACTCTG                         GGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCA
genomic: TGTCAAAAACAATGTATCTAG-AAGACCGAACTGTACGTTTACAACTCTGgtaagtatca ... ttgctgtcagGG-ATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCA
EST: gi|211481374|gb|FL368109.1|FL368109
EST:     CTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTG                         GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAG
genomic: CTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTGgtaagtatca ... ttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAG

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 4 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 42 (downstream exon)
Score: 7

GCAACGATTGGCATTGACTTTCTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTGgtaagtatca ... ttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 14

GCAACGATTGGCATTGACTTTCTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTGgtaagtatca ... ttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA


Block sizes: 41 (upstream exon), 26 (downstream exon)
Score: 3

GCAACGATTGGCATTGACTTTCTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTGgtaagtatca ... ttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 158

GCAACGATTGGCATTGACTTTCTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTGgtaagtatca ... ttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
                                       ttgttctt  CT-rich tract
        ttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA

- - - - - - - - - - - - - - - - - -ttttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcatt