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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacacggtttattcaaagtttctttgaccagatgtgtttcattcctagagtttgtaaatgaactcgaatgattgtttattaatgtgttgattttttgctgtacag

Basic information

species Glycine max
transcript GLYMA13G20930.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20930.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 5'ss of exon 8
GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacacggtttattcaaagtttctttgaccagatgtgtttcattcctagagtttgta--aatgaactcgaatgattgtttattaatgtgttgattttttgctgtacag---------------
| ||||||||||||  |||  |||| ||||| |||||| ||||||||||||| || || |||||||||||||| || || ||||||     |    |||     |  | ||   |       ||||   | ||  |   ||  |  ||||||| ||    ||||| || |  ||| ||| | |||   |   ||                
GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAGgtatg---ataaattaacatcatatcctgaaatacagcctgttgattgccgtgttcttaaaccaatgaacccg--ctattgtgtaattgtgtattg-tatttcattacgcaacattccgttttgcag

upper sequence: GLYMA13G20930.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 8
GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacacggtttattcaaagtttctttgaccagatgtgtttcattcctagagtttgtaaatgaactcgaatgattgtttattaatgtgttgattttttgctgtacag
| ||||| ||||||  |||| |||| ||||| |||||| |||||||||||||||| ||||||||||||||||| || || ||||||    ||   |    |||||  ||  |    |   |||  |   |  ||   || ||||  |   ||  ||       ||   | | |  | ||   || |       
GTTCTGTGAATGCAGCCAACTGTGCGGAGCTAGCAAAGAAAGAAGATATTGATGGTTTTCTTGTTGGTGGTGCCTCTTTGAAGgtatg-gcaaactaacctcaaacctttgtattacttctgttgtcagtagctgccgtctgtagct---ctttaaactcctcttgcaactttcatcatgcgtttcc------

upper sequence: GLYMA13G20930.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM5G852968_T03 (Zea mays), 5'ss of exon 8
GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacacggtttattcaaagtttctttgaccagatgtgtttcattcctagagtttgtaaatgaactcgaatgattgtttattaatgtgttgattttttgctgtacag
| ||||| ||||||  |||| |||| ||||| |||||| |||| ||||| ||||| ||||||||||||||||| || || ||||||    ||   |    |||||   ||||||  || |      |   ||||  |  || ||  |   |   |     ||  | |   | | |  |  |  |  || |   
GTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatg-gcaaattaacctcaaa---tctttgtacataatctcctttgtcctgtaccttcta--ttgtcagtagctgctgcctgtagctct-taaagctcatcttgca---

upper sequence: GLYMA13G20930.1 (Glycine max), 5'ss of exon 8
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 5'ss of exon 7
GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacacggtttattcaaagtttctttgaccagatgtgtttcattcctagagtttgtaaatgaactcgaatgattgtttattaatgtgttgattttttgctgtacag
| ||||| |||| | |||||||||| |||||||| ||  ||||||| |||||||||||||||||||||||||| || || |||||| |   |  |||||  |       ||||    | ||||  || ||   ||||    |||||  | |||  |      ||||||       |                 
GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaaaagtaaagtttagac-------ctttatggatatgttgttgatgaatagaa---gtaaagcagctcacactcacctttattgtgactctag---------------

upper sequence: GLYMA13G20930.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 5'ss of exon 8
GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacac--acggtttattcaaagtttctttgaccagatgtgtttcattcctagagtttgtaaatgaactcgaatgattgtttattaatgtgttgattttttgctgtacag
| || || ||||  |||||  || | ||||| || || ||||| ||||||||||||||||||||||| |||||||| ||||||||| |     || |||      ||   |   | || ||     ||| |   ||| |  |  ||||  ||  |  |||||     | | |       |||||  |   |    
GTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAGgtatatttttactgttgggcttaaaaattaataactag-----tttga---ctaaaagtaataaagaaaaacttatgataaaaaacttacaaaaaaattttaggagct----

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|208286741|gb|GE085315.1|GE085315
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
EST: gi|208199925|gb|GD998612.1|GD998612
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
EST: gi|193565354|gb|FK522821.1|FK522821
EST:     AAAGCAAGAAGATATTGATGGATTTCTTGGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACC
genomic: AAAGCAAGAAGATATTGATGGATTTCTTG-TTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACC
EST: gi|208158835|gb|GD958252.1|GD958252
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
EST: gi|193716815|gb|FK654653.1|FK654653
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATT
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATT
EST: gi|207752026|gb|GD722143.1|GD722143
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
EST: gi|208133444|gb|GD929123.1|GD929123
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAA
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAA
EST: gi|208220559|gb|GE017135.1|GE017135
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATC
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATC
EST: gi|193532323|gb|FK491989.1|FK491989
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTAC
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTAC
EST: gi|193404769|gb|FK368282.1|FK368282
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATTCAG
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAG
EST: gi|207841384|gb|GD811420.1|GD811420
EST:     AAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCAATTAAAG                         GGTCCTGAGTTTGCTACCATTATC
genomic: AAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCA-TTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATC
EST: gi|151399754|gb|EV269625.1|EV269625
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
EST: gi|207816408|gb|GD786241.1|GD786241
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTGGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
EST: gi|208215434|gb|GE012463.1|GE012463
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATT
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATT
EST: gi|193632944|gb|FK580092.1|FK580092
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTT
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTT
EST: gi|193679131|gb|FK620625.1|FK620625
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
EST: gi|193703433|gb|FK636505.1|FK636505
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTATC
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATC
EST: gi|208240804|gb|GE036834.1|GE036834
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGTTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTATCAATTCAGTCACTTCCAAGAAAGTTGCG
EST: gi|193730132|gb|FK663090.1|FK663090
EST:     CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG                         GGTCCTGAGTTTGCTACCATTAT
genomic: CAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacac ... tgctgtacagGGTCCTGAGTTTGCTACCATTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacacggtttattcaaagtttctttgaccagatgtgtttcattcctagagtttgtaaatgaactcgaatgattgtttattaatgtgttgattttttgctgtacag

- - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG