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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccatttaatcaaacactttgttttccattcatctattctctctctctctctctctcattcgaaaaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATATTGCAACTGTTTTGAACAGAGCTTGGGCTGCCGGCGTCACCCGAATTAT

Basic information

species Glycine max
transcript GLYMA19G38780.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G38780.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 2
----------------------------------gtgagccatttaatcaaacactttgttttc-cattcatctat-----tctctctctctctctctctcattcgaaaaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATATTGCAACTGTTTTGAACAGAGCTTGGGCTGCCGGCGTCACCCGAATTAT
                                    |      |      |     | | | || |  |  ||||      |||  |||| |    ||   || ||||  |  |  |||||||||||| | ||| |||||||||||||||||||| |||| | | || ||  |  | ||  |   | | || ||||| |||||||||  ||| || ||
gtacccacctcctcctctcctcacgattcttatctcgtttttctcggctcactgtctggctctcacgcttttctacttgcgtcttgctctttgctgctgcgatgcgaacgaactgaagATGGCATGTTCAGGGGCATCTACCACGGCAAGCAATGCCACGCCGCCGACATCCCCGCCGTGCTCGCCCGCGCGTGGGCGGCCGGCGTCGACCGCATCAT

upper sequence: GLYMA19G38780.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 1
----------------------------------gtgagccatttaatcaaacactttgttttc-cattcatctat-----tctctctctctctctctctcattcgaaaaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATATTGCAACTGTTTTGAACAGAGCTTGGGCTGCCGGCGTCACCCGAATTAT
                                    |      |      |     | | | || |  |  ||||      |||  |||| |    ||   || ||||  |  |  |||||||||||| | ||| |||||||||||||||||||| |||| | | || ||  |  | ||  |   | | ||  |||| |||||||||  ||| || ||
gtataaccgccgcctcctcctcccgattcttatctcgtttttctcggctcactgtctggctctcacgcttttctacttgcgtcttgctctttgctgctgcgatgcgaacgaactgaagATGGCATGTTCAGGGGCATCTACCACGGCAAGCAATGCCACGCCGCCGACATCCCCGCCGTGCTCGCCCGTGCGCGGGCGGCCGGCGTCGACCGCATCAT

upper sequence: GLYMA19G38780.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------gtgagccatttaatcaaacactttgttttccattcatctat-tctctctctctctctctct--------------------cattcgaaaaatttac--------------agATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATATTGCAACTGTTTTGAACAGAGCTTGGGCTGCCGGCGTCACCCGAATTAT
                                           |  ||   |||       | | | ||    | | ||| | |||||||||||||| ||||                    | | ||     ||| |              |||||||||||| ||||| ||||||||||||||||| || |||| | | || ||  |  | ||  |     | || |||||||| ||||||   || || ||
gtaactcaaataccctccgtttcgctcttttcttagtgcttacgtacctcgtaactggttgcct-gcttcttgtgcctctctctctctctctctctccctcttcccgcgtggcgtgcgccgccgtacgggctgtttgctgctactgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT

upper sequence: GLYMA19G38780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0032g01170.t01 (Vitis vinifera), 3'ss of exon 2
gtgagccatttaatcaaacactttgttttccattcatctattctctctctctctctctctcattcgaaaaattta--------cagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATATTGCAACTGTTTTGAACAGAGCTTGGGCTGCCGGCGTCACCCGAATTAT
|| || |||||  || ||||| | ||   ||||     | |    | | | | |   ||||| ||   ||||| |        |||||  |||||| |||||||||||| | |||||||| || ||||| || ||| ||||| | || |||| ||||||||||  ||| || ||     |||||||
gtcaggcatttcttcgaacacatggtggcccatatgcttctctattttgtttatgcttctcaatctgcaaattcaacctctgacagATAACATGTTCAAGGGAATCTACAATGGCAAGCAGTGCCACGTGTCTGATCTTGCAGCAGTGTTGAGCAGAGCTTGGAGTGCTGGTGTTGATAGAATTAT

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|151396286|gb|EV266163.1|EV266163
EST:     AGATATAGCCGTCAACTTCACCG                         ATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
genomic: AGATATAGCCGTCAACTTCACCGgtgagccatt ... aaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
EST: gi|192332143|gb|FK026381.1|FK026381
EST:     ATAGATATAGCCGTCAACTTCACCG                         ATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
genomic: ATAGATATAGCCGTCAACTTCACCGgtgagccatt ... aaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
EST: gi|298194140|gb|HO040788.1|HO040788
EST:     ATAGATATAGCCGTCAACTTCACCG                         ATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
genomic: ATAGATATAGCCGTCAACTTCACCGgtgagccatt ... aaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
EST: gi|298166829|gb|HO010268.1|HO010268
EST:     ATAGATATAGCCGTCAACTTCACCG                         ATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
genomic: ATAGATATAGCCGTCAACTTCACCGgtgagccatt ... aaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
EST: gi|120492279|gb|EH220446.1|EH220446
EST:     ATAGATATAGCCGTCAACTTCACCG                         ATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
genomic: ATAGATATAGCCGTCAACTTCACCGgtgagccatt ... aaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
EST: gi|192323850|gb|FK015631.1|FK015631
EST:     ATAGATATAGCCGTCAACTTCACCG                         ATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA
genomic: ATAGATATAGCCGTCAACTTCACCGgtgagccatt ... aaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttccattcatctattctctctctctctctctctcattcgaaaaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATATTGCAACTGTTTTGAACAGAGCTTGGGCTGCCGGCGTCACCCGAATTAT
                                      attcgaaaaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccatttaatcaaacactttgttttccattcatctattctctctctctctctctctcattcgaaaaatttacagATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATATTGCAACTGTTTTGAACAGAGCTTGGGCTGCCGGCGTCACCCGAATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT