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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttttacccttcttatgtataagattagtttatacttctatttcttctggccatgtgtaagaaacagtgaaaacaagcttaattttgtttttcctgattcttttttctttgtaataatcagatatgaatattttgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAAGGTTGATACTGGTGGATATTGTTCTCTGGACGATGTAACTAGTGTTCCT

Basic information

species Glycine max
transcript GLYMA13G28910.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G28910.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G150201_T03 (Zea mays), 3'ss of exon 5
gtatgcttttacccttcttatgtataagattagtttatacttctatttcttctggccatgtgtaagaaacagtgaaaacaagcttaattttgtttttcctgattcttttttctttgtaataatcagatatgaatattttgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAAGGTTGATACTGGTGGATATTGTTCTCTGGACGATGTAACTAGTGTTCCT
                                                             ||||||     ||   ||   ||   |||   | ||| | | ||  | ||     |  |||||   |       | |      |||| ||| |||| ||||||||||| |||||| | |||||||| ||  ||||||| |||||| ||||||| ||    ||  |||| ||||| || ||  | |||
-------------------------------------------------------------gtaagattt--tggtgactgcctacttttcagtcttcatcaatcactgtt-----tgctaatccttttcttccttctccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAAAGTTGATTCTGGTGGTTACACATCATTGGATGATGTCACAAGCCTACCT

upper sequence: GLYMA13G28910.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G30000.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcttttacccttcttatgtataagattagtttatacttctatttcttctggccatgtgtaagaaacagtgaaaacaagcttaattttgtttttcctgattcttt----tttctttgtaataatcagatatgaatattttgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAAGGTTGATACTGGTGGATATTGTTCTCTGGACGATGTAACTAGTGTTCCT
                                                           || | | ||  | | |   |    ||    |   |  ||    |||||      |  | |    | |      |   || | |    || |||||| || ||    ||||||||||| |||||||||||||||||  ||||||||||  |  | ||||||||    ||  |||| ||||||||    || |||
-----------------------------------------------------------gtatgaaaactattca--tccgattttccctcactaatctaagttcttggggactattctactcttaaagctaacacatttctaaaattgcagATACCGAGATCAAGGTTGGCAAATTTTTGAAGCTTTTGAAAAGTACACAAAGGTGAAATCAGGTGGATACACATCATTGGATGATGTAACAGAAGTGCCT

upper sequence: GLYMA13G28910.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0003g03280.t01 (Vitis vinifera), 3'ss of exon 5
gtatgcttttacccttct-tatgtataagattagtttatacttctatttcttctggccatgtgtaagaaacagtgaaaacaagcttaattttgtttttcctgattcttttttctttgtaataatcagatatgaatattttgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAAGGTTGATACTGGTGGATATTGTTCTCTGGACGATGTAACTAGTGTTCCT
||||| |||||   || |  | | || | |||  ||| |  | | || |    || |||| |           |  | | |   ||   | ||  |||  |  | ||| |||  || || | ||||  |||      ||||||   ||||||||| |||||||| ||||| ||||||||||| |||||||| ||||| ||||||||| |||| |||||  |||||||||| ||||| || ||  |||||
gtatgtttttaaggttttgcaggcattacattgttttcttatacaatcttcattgtccatat-----------tatacatagtttt---tctgcatttttttgtacttctttagttcta-tgatcaactattgtctatttgtg---cagATATCGTGAATGGGGCTGGCAGATCTTTGAAGCATTTGAAAAACACACGAAGGTTGATTCTGGAGGATACAGTTCTCTGGATGATGTCACCAGGCTTCCT

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|17400772|gb|BM177554.1|BM177554
EST:     GAGACCGTGGAGTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAA                         ATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAA
genomic: GAGACCGTGGAGTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAAgtatgctttt ... tgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAA
EST: gi|7588505|gb|AW704361.1|AW704361
EST:     GAGACCGTGGAGTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAA                         ATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAA
genomic: GAGACCGTGGAGTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAAgtatgctttt ... tgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAA
EST: gi|23726311|gb|BU761144.1|BU761144
EST:     GAGACCGTGGAGTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAA                         ATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAA
genomic: GAGACCGTGGAGTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAAgtatgctttt ... tgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAA
EST: gi|254338683|gb|GR849994.1|GR849994
EST:     GAGACCGTGGAGTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAA                         ATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAA
genomic: GAGACCGTGGAGTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAAgtatgctttt ... tgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAA
EST: gi|6455624|gb|AW186307.1|AW186307
EST:     GAGACCGTGGAGTCATTGTTGGTTT-GTGCCGTATCACAGAAGAACCAAA                         ATATCGGGAAATGGGGT
genomic: GAGACCGTGGAGTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAAgtatgctttt ... tgtgttacagATATCGGGAA-TGGGGT
EST: gi|10254345|gb|BE822111.1|BE822111
EST:     GTCATNGTTTGTTTTGTANNNTATCACAGAAGATCCAAA                         ATATCGGGAATGGGGNNNGCANATCTTTGAAGCTTTTGAAAATCACACAAA
genomic: GTCATTGTTTGTTTTGTACCGTATCACAGAAGATCCAAAgtatgctttt ... tgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctgattcttttttctttgtaataatcagatatgaatattttgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAAGGTTGATACTGGTGGATATTGTTCTCTGGACGATGTAACTAGTGTTCCT
   tcctgat  putative branch site (score: 3)
            ttttttctttgtaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttttacccttcttatgtataagattagtttatacttctatttcttctggccatgtgtaagaaacagtgaaaacaagcttaattttgtttttcctgattcttttttctttgtaataatcagatatgaatattttgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAAGGTTGATACTGGTGGATATTGTTCTCTGGACGATGTAACTAGTGTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA