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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaacaaacaaccgacgctcttactagcattcacaatatcatcacatgcatgcatgttgatactccgtatatatatgcatgcag

Basic information

species Zea mays
transcript GRMZM2G122172_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122172_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g39230.1 (Oryza sativa), 5'ss of exon 7
GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtg-----cgtaacaaaca---accgacgctcttactagc---attcacaatatc---atcacatgcatgcatgttgatactccgtatatatatgcatgcag
|| |||||| |||| |||| ||||||||||||||| ||||||||||||||||||||||||||||       |  | | | |   | || |   ||  ||||    || |||  || |   |||||   | ||    |  |     | |    ||   |||| | 
GACGACATGGTCATCGCGAGGGAGGAGATCTTCGGCCCCGTCATGTGCCTGATGAAGTTCAAgtaaacccagctatatatatggatcgccatcctctctagtcaaatacacggtacctttatcactaacttgtggatccagggatcat-cggatccacatgta-
















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|5005600|gb|AI711662.1|AI711662
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GCCGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|148942564|gb|EC887583.2|EC887583
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|76020436|gb|DT947606.1|DT947606
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|78083932|gb|DV512325.1|DV512325
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|149087182|gb|EE176719.2|EE176719
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|4835135|gb|AI670361.1|AI670361
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|78074898|gb|DV503332.1|DV503332
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|148959027|gb|EC905199.2|EC905199
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|211155790|gb|FL451802.1|FL451802
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|148948769|gb|EC894170.2|EC894170
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|78091392|gb|DV519766.1|DV519766
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|71317747|gb|DR795632.1|DR795632
EST:     ATAGCGAAGGAGGAGATCCTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|148950305|gb|EC895864.2|EC895864
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|33468129|gb|CF245178.1|CF245178
EST:     TAGCGAAGGAGGAGATCTTCGGACCTCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGAT
genomic: TAGCGAAGGAGGAGATCTTCGGACC-CGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGAT
EST: gi|148993480|gb|EE033799.2|EE033799
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
EST: gi|71426117|gb|DR807167.1|DR807167
EST:     ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA                         GACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG
genomic: ATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGG

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 3 RNA-Seq libraries.


Block sizes: 35 (upstream exon), 39 (downstream exon)
Score: 7

GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGGGGCGGGGGTGGTGACGCGGGACCTGGACGTGGCGAACCGGGTGGTGAGG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 18

GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGGGGCGGGGGTGGTGACGCGGGACCTGGACGTGGCGAACCGGGTGGTGAGG


Block sizes: 44 (upstream exon), 37 (downstream exon)
Score: 7

GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaaca ... atgcatgcagGACGGTGGAGGAGGCGATCGCGAGGGCGAACGACACGCGGTACGGGCTGGGGGCGGGGGTGGTGACGCGGGACCTGGACGTGGCGAACCGGGTGGTGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAAgtgcgtaacaaacaaccgacgctcttactagcattcacaatatcatcacatgcatgcatgttgatactccgtatatatatgcatgcag

- - - - - - - - - AAGGAG
- - - - - - - - - - GGAGGA
- - - - - - - - - -  GAGGAG
- - - - - - - - - - - AGGAGA
- - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - GAGATC