Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtgtaccttgctccatgtgatggatgatcgttacttatgttcgtcttgcttctgcggcggctgattgaatggctgtgcctccgtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCA

Basic information

species Zea mays
transcript GRMZM2G177445_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177445_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g61010.1 (Oryza sativa), 3'ss of exon 2
gtccgtgta-ccttgctccatgtgatggatgatcgttacttatgttcgtcttgcttctgcggc-ggctgattgaatggctgtgcctccgtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCA
|| |||| | | ||||||||| ||       |||  | |||   ||    | ||  || ||   |  ||  |   |   || |  |  ||| ||||||||||||||||||||||| ||||||||||| |||| | |||||||||| |||||||| |||||||||||||  |||||||| || |||||||| |||||||
gttcgtgcagctttgctccatctgc------atcagtgcttgccttgccttcgccgcttcgattgaatggctccgttcttgcgtgtgtgtgtgtgcagGAGGAGGCGAGGGCTGTCGGGCAGCTGCGGAGTGTCCGGCTGGCCAACCTGATCGGCTGCTGCTGCGAGAATGGCGAGCGGCTGCTCGTCGCGGAGTTCA
















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|101385419|gb|EB814755.1|EB814755
EST:     CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|211337353|gb|FK979584.1|FK979584
EST:     CATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCCAGTTCCTG                         GAGGAGGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCC
genomic: TATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCC-AGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGG-CGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATC-
EST: gi|149023559|gb|EE045892.2|EE045892
EST:     CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|148967635|gb|EE018892.2|EE018892
EST:     CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|148996262|gb|EE035542.2|EE035542
EST:     CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|76281723|gb|DV021291.1|DV021291
EST:     CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|211335198|gb|FK979578.1|FK979578
EST:     CCATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTG
EST: gi|211337351|gb|FK979582.1|FK979582
EST:     CCATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|211337354|gb|FK979585.1|FK979585
EST:     CCATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|93284518|gb|EB676782.1|EB676782
EST:     CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|71440119|gb|DR821169.1|DR821169
EST:     CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|211337362|gb|FK979593.1|FK979593
EST:     CCATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCC
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCC
EST: gi|211337357|gb|FK979588.1|FK979588
EST:     CCATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGG
EST: gi|211337360|gb|FK979591.1|FK979591
EST:     CCATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|211337355|gb|FK979586.1|FK979586
EST:     CCATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|71447053|gb|DR828103.1|DR828103
EST:     CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|148931103|gb|EC873754.2|EC873754
EST:     CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
EST: gi|211337356|gb|FK979587.1|FK979587
EST:     CCATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTG                         GAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG
genomic: CTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTG

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: 44 (upstream exon), 42 (downstream exon)
Score: 14

ACCCAACGTGGTCTACCGTGGCACGCTCTTCAGCTCCGGCCGCACCGTCGCTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCA


Block sizes: 11 (upstream exon), 39 (downstream exon)
Score: 1

ACCCAACGTGGTCTACCGTGGCACGCTCTTCAGCTCCGGCCGCACCGTCGCTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCA


Block sizes: 21 (upstream exon), 39 (downstream exon)
Score: 3

ACCCAACGTGGTCTACCGTGGCACGCTCTTCAGCTCCGGCCGCACCGTCGCTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCA


Block sizes: 39 (upstream exon), 28 (downstream exon)
Score: 5

ACCCAACGTGGTCTACCGTGGCACGCTCTTCAGCTCCGGCCGCACCGTCGCTATTAAGCGCTTCGGCCGCTCCGCCTGGCCGGACTCACGCCAGTTCCTGgtccgtgtac ... gtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcgtcttgcttctgcggcggctgattgaatggctgtgcctccgtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCA
                     ggctgat  putative branch site (score: 5)
                                        cctccgt  putative PPT
                          attgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtgtaccttgctccatgtgatggatgatcgttacttatgttcgtcttgcttctgcggcggctgattgaatggctgtgcctccgtgggtgcagGAGGAGGCGAGGGCTGTTGGGCAGCTGCGTAGTGGCAGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC