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

gtaaaaacattgtgatgaggaagaaccttttgttggataaagaatttcagtttgatatcgagtaacttccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG

Basic information

species Glycine max
transcript GLYMA10G12350.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G090689_T01 (Zea mays), 3'ss of exon 3
------------------------------------gtaaaaacattgtgatg--aggaagaaccttttgttggataaaga-----atttcagtttg-atatcgagtaacttccctt---tgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
                                     | ||| | || |  ||  ||  | | |  |    |||   || |      ||| | |||  |||| |      |||||||   | |||||| |||||  ||||| |||| ||||| || || ||||| || ||||| ||||||||||| ||||||||||  || | ||  |
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagtgaaagctgtaaactggtccaacatgcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG

upper sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G006753_T01 (Zea mays), 3'ss of exon 3
------------------------------------gtaaaaacattgtgatgaggaagaaccttttgttggataaag--aatttcagtttgatatcgagtaacttccctt---tgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
                                     | ||| | || |  |||           | ||   | |       ||| | ||  |||| |      |||||||   | |||||| |||||  ||||| |||| ||||| || || ||||| || ||||| ||||||||||| ||||||||||  || | ||  |
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG

upper sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaaaacattgtgatgaggaagaaccttttgttgg----ataaagaatttcagtttgatatcgagtaacttccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
           || ||     |     | || | |      |  ||  | | ||||   |      ||  ||  |||  |||||||||||| ||||||||||| || || || || ||||| |||||||| ||||| || ||  |||||||||  || || || |
-----------gtaattcatcatcctttcttttcgatattgttgaggttgtgagttgatttatatatatattttcttcccagGCTATTCTGCTCAATGCTTTGCTCGGACCCCAAGCTTGATTCACACCGTTTCAAAGACATGCTTGATGAGGCCATTGCAGCAG

upper sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
gtaaaaacattgtgatgaggaagaaccttttgttggataaagaatttcagtttgatatcgagta-acttccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
||| ||         ||        | |||| ||   | | |  |  | | |     || | |   ||| ||||  |||||| |||||||||||||||||||| || ||||| || || ||||||||||||||||||||| |||||||||  ||| | || |
gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG

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|208312400|gb|GE110336.1|GE110336
EST:     ATCTGTACAAGTTAAGTTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGAATCCTAAACTTGACTCACACCGAT
genomic: ATCTGTACAAG--AAG-TGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAG-ATCCTAAACTTGACTCACACCGAT
EST: gi|207792619|gb|GD767381.1|GD767381
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAA
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAA
EST: gi|151412912|gb|EV282724.1|EV282724
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|151396151|gb|EV266028.1|EV266028
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|41145363|gb|CK605574.1|CK605574
EST:     AAAAATGATTTGATTGATCTGTACGAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|208237877|gb|GE040365.1|GE040365
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|298194691|gb|HO043163.1|HO043163
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|192323158|gb|FK017384.1|FK017384
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|207758651|gb|GD728697.1|GD728697
EST:     CTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: CTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|151402844|gb|EV272657.1|EV272657
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|207787948|gb|GD762544.1|GD762544
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|151407863|gb|EV277678.1|EV277678
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATTCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|208130358|gb|GD928131.1|GD928131
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT
EST: gi|16346108|gb|BI971703.1|BI971703
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAG                         GTTANNNNNNNCAATGCTTTGTTCAGATCCTAAACTTGACTCACTCCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccttttgttggataaagaatttcagtttgatatcgagtaacttccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
                                    gagtaac  putative branch site (score: 2)
                                          cttccctttgc  CT-rich tract
             ataaagaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaacattgtgatgaggaagaaccttttgttggataaagaatttcagtttgatatcgagtaacttccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT