Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgccccatctggtcgttcctgctcgatctgggcgcagtctggtttcttgatctgtatcgcgctcttggttgtattgatggcttcgctggatttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG

Basic information

species Zea mays
transcript GRMZM5G820996_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G820996_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
------gttcgccccatctggtcgttcctgctcgatctgggcgcagtctggtttcttgatctgtatcgcgctcttggttgtattgatggcttcgctggatttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
       | ||  |   || |  |    | || | |    ||   || ||||||||||||||||  |    |  || |    ||| ||| |    ||  || |||||||||||| |||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||||||
gtacggatccgttcttgcttgaagaattttcttgtt----gcctggtgtggtttcttgatctgttgcagatttgtgatgtgtttggtgg-tggattg--ttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG

upper sequence: GRMZM5G820996_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G14980.1 (Glycine max), 3'ss of exon 1
-------------gttcgccccatctggtcgttcctgctcgatctgggcgcagtctggtttcttgatctgtatcgcgctcttggttgtattgatggcttcgctggatttt---tgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
             | ||||  |   | ||||||  | |||  ||  ||||     |     |      ||| ||      | |  |||| || ||   | ||||| | ||   ||||||||| |||||||| || ||   ||| ||||||||||| ||||| ||||||||||| ||||| || |||| ||| || |||
gtaaactgtcttcgctcgcttcgcatcgtcgtttattctcactcatggcgtgtcgtttgcgccgcgagtgt-tctaaaaatagactgtaatg-tgcggtggctggttgttgaatgcagGTGGCAAGCTTGTTTATCAGACCACGAAGAAGAGGGCCAGCGGACCCAAGTGCCCTGTCACTGGAAAGAGGATTCAAGGG

upper sequence: GRMZM5G820996_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G41280.1 (Glycine max), 3'ss of exon 1
-----------------gttcgccccatctggtcgttcctgctcgatctgggcgcagtctggtttcttgatctgtatcgcgctcttggt---tgtattgatggct--tcgctggatttt---tgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
                 | ||||| ||  | ||||||  | |||  ||  |||||  | | ||||   |         | ||||        | | || |||     | ||||  | ||   ||||||||| |||||||| || ||   ||| ||||||||||| ||||| ||||||||||| ||||| || |||| ||| || |||
gtaaataaactctcttcgctcgcctcacatcgtcgtttattctcactcacggcgcgttgtcgttttgcgccgccgcgagggctccaaaaatatattttaatgtgcggttgctgattgttgaatgcagGTGGCAAGCTTGTTTATCAGACCACGAAGAAGAGGGCCAGCGGACCCAAGTGCCCTGTCACTGGAAAGAGGATTCAAGGG

upper sequence: GRMZM5G820996_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G05740.1 (Glycine max), 3'ss of exon 1
---------------------------------------gttcgccccatctggtcgttcctgctcgatct---gggcgcagtctggtttcttgatctgtatcgcgctcttggttgtattgatggcttcgctggatttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
                                       |  |      | |  | |||  || |   | |         ||| |    | || ||  ||   ||    |  ||  | ||  ||| |  |  ||| |  ||||||||||||||| || || ||    |||||||||||||| ||||| ||||||||||||||||| || |||| ||| ||||||
gtaatcaaatccctccctcactgattatgcttcggatcggaacaatttttgtttttgtttttgttttgttttaaaaaaaaagtttttggtattaattggttctgctgggtacgtcttgtt--tggttctgtgggaataatgcagGTGGGAAGCTCGTTTATCAGACTACCAAGAAGAGGGCCAGCGGACCCAAGTGCCCCGTCACTGGCAAGAGGATTCAGGGG

upper sequence: GRMZM5G820996_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G11920.1 (Glycine max), 3'ss of exon 1
----------------------gttcgccccatctggtcgttcctgct-cgatctgggcgcagtctggtttcttgatct---gtatc-----gcgctcttggttgtattga---tggcttcgctggatttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
                         | | |   ||  ||| |  |||| |||   ||    | | | | || || || |   ||||      |  ||   || | | |||    |||    |  ||| |  ||||||||||||||| || || ||   ||||||||||||||| ||||| ||||||||||||||||| || |||| ||| ||||||
gtaatcaaatccctcttcggaacccctcactcactcttcgattatgcttcgaatcggaacaatttttgctttttaattttgggtattaattggttctgacgggtatgttgtgtttggtgatgtgggaataatgcagGTGGGAAGCTCGTTTATCAGACCACCAAGAAGAGGGCCAGCGGGCCCAAGTGCCCCGTCACTGGCAAGAGGATTCAGGGG

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|211533043|gb|FL043886.1|FL043886
EST:     TCACAGCTACGCGACNNVATCCAATCAGACCCGGGTCGTGAAGACCC-AG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|30088131|gb|CB886336.1|CB886336
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|15589458|gb|BI674074.1|BI674074
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|211533045|gb|FL043888.1|FL043888
EST:     CACAGCTACGCGACAAAATCCAATCASRACCCGGGTTGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCA
genomic: CACAGCTACGCGACAAAATCCAATCAG-ACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCA
EST: gi|211352603|gb|FL470915.1|FL470915
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|211533048|gb|FL043891.1|FL043891
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|60348609|gb|DN215582.1|DN215582
EST:     TCACAGTTACGGGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|31405586|gb|CD484318.1|CD484318
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|211530048|gb|FL043882.1|FL043882
EST:     SACAGCTACGCGACAAAATCCAATCARKACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: CACAGCTACGCGACAAAATCCAATCA-GACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|15313100|gb|BI478560.1|BI478560
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|211533047|gb|FL043890.1|FL043890
EST:     TACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|30306493|gb|CD001166.1|CD001166
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|60357248|gb|DN224221.1|DN224221
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|26557730|gb|CA829965.1|CA829965
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|60395053|gb|DN227922.1|DN227922
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|16927550|gb|BM080619.1|BM080619
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|211533046|gb|FL043889.1|FL043889
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|60345851|gb|DN212824.1|DN212824
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|60354426|gb|DN221399.1|DN221399
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
EST: gi|30087140|gb|CB885348.1|CB885348
EST:     TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAG                         GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT
genomic: TCACAGCTACGCGACAAAATCCAATCAGACCCGGGTCGTGAAGACCCCAGgttcgcccca ... atttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatctgtatcgcgctcttggttgtattgatggcttcgctggatttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
                           tattgat  putative branch site (score: 3)
                                              tttttgc  putative PPT
                                             attttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgccccatctggtcgttcctgctcgatctgggcgcagtctggtttcttgatctgtatcgcgctcttggttgtattgatggcttcgctggatttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG