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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT

Basic information

species Glycine max
transcript GLYMA04G37920.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 2
gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgc--acttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                               | || ||   | |    || ||||        | | |  | ||| | |    || | |   ||| ||||  | | |    |  |||  | | | ||   ||| |||||||| |||||||||| | | ||||| || ||||||||||||||||| ||| ||||||| || |||||||| | ||| ||||| |||||||| || ||||
---------------------------------------------------------------ttaatca---tctaccctgattggcaccttctatcat--actttgtgcccacat-tctctttggttatttcagcgtattgatcttttgcttctgttattgtttcagGAAGAAAAGGCAATTGGACGTGGAATCCTCCCATTGCTTCAGCGTGCCACCCTGGTTCAGACCTTTGGACAAAAGAACCATGTCTGCTTGAAGGACGGCT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 2
------gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaaca-tgcactttta-tcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
       ||      ||  | |  | | |||  |      |  |  ||||| ||    ||| | |  |||  |          | || ||  |  | | | | ||  |  |  || || |  |  || | |   |||| | | | ||||  |  | |  |  | |  | || ||||||||||| || |||||  | || || ||||||||||| |  ||||| || ||||||||||| |||||||||| ||| |||||||||||||| ||||| |
gtaatgatatattggtttatttgtcttcttacctgccaagtccttgtcactgttgtagctagtcatgattttagttccaca-atagttttaagaaataggtagctcaggatagatcctacctttagtccctatctattctgaaactgcatatgcaatggttatatgtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g32670.1 (Oryza sativa), 3'ss of exon 2
---------------------gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgt--ggtgtt--tggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaaca-tgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                      |   | |||| |  |    | |   |  | || |||        ||| |||   ||  || ||   ||| |   | |  | |||    | | || |  |      |||||   |||   ||   ||| |  |  || |  | ||   ||   |  ||| |     ||  ||||||| || || |||||  | |||||||| || ||||| || |||||||| ||||| |||||||||||||||  ||| ||||| ||||| |||||||| |
gtgtgtgctaattcccttggcatctcacatttggatttgtctgtgtgtaattctctttctgatttcatt-gtttactttggagtttggacatacccttttagatgtcaacgctaaggataaaacattattttgaccttttctactcacaag--ttctgaagtagtgttattaactgttgtatactatttgtagGAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACGTTGGTCCAAACATTTGGACAGGAGAACCATGTTTGCTTAAAAGAGGGTT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 2
gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                   | || ||  ||   |||| | |       | |    |         ||   | | | |  |||||||| |  ||   |  ||||||| | ||||  | |          || |||||||||||| || |||| | | ||||| ||||| ||||||||||||||||| |||||||| || |||||||||| ||| ||||| ||| |||| || || |
---------------------------------------------------tttagtagaaa---aaaccactcactaaatttccaattgacta---ctgttactgtctgtttcaatatcttgatattt-ctgtaacaagtacttcaaac---------tgtaccagGAAGAGAAAGCCATTGGACGGGGAATCCTTCCCTTGCTTCAGCGTGCTACGTTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGATGGGT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G023020_T01 (Zea mays), 3'ss of exon 2
gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccg---ttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                               | |     |   ||   |   | ||| | ||   ||||  ||||| |     | |  |||||     |   ||  || |  | || |   | | || |   ||||||||||| || || || ||  | ||||||||||||||||| |  |||||||| ||||| ||||| |||||||||  ||||||||| ||| |||| ||||| |
--------------------------------------------------------------gtgaggttcaccatgcttttcattgtgtgcag--tcttgccttttaatgcctta-acttacattttactcacaagttgtatgtgtaacgattgtatcggcatttccagGAAGAAAAAGCTATCGAGCGTGGAATTCTTCCATTGCTGCGACGTGCTACATTGGTCCAAACCTTTGGACAGGAGAATCATGTTTGCCTGAAGGAGGGTT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G000581_T01 (Zea mays), 3'ss of exon 2
gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                             ||    |||| |||       |   ||  | |         | |   |  | ||| || |  ||   |  |||||||    |  ||  ||  || ||    | ||||||||||| ||||| |   | ||||| ||||| |||||||||||||||||  ||||||| || |||||||||| ||| ||||| ||| |||| |  || |
------------------------------------------------------------tataatgacaacttgctaaacttccagttggcaccttacattactggctgttccaacatctcgatattt-ctgtaacacaagcgctt--caaattatt----ttcagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACACTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGGCGGGT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G141094_T01 (Zea mays), 3'ss of exon 7
gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                  | || |||  |      |||| || |   ||   |||        |  |   | |   |  | ||| || |  ||   |  |||||||    |  ||  ||  || ||    | ||||||||||| ||||| |   | ||||| ||||| |||||||||||||||||  ||||||| || |||||||||| ||| ||||| ||| |||| |  || |
--------------------------------------------------tactgttataat----gacaacttttccagt---tggcaccttacattt---actggctgttccaacatctcgatattt-ctgtaacacaagcgctt--caaattatt----ttcagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACACTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGGTGGGT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G301552_T01 (Zea mays), 3'ss of exon 9
gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                 || || |||  |      |||| || |   ||   |||        |     |  | |    | ||| || |  ||   | ||||||||    |  ||  ||  || ||    | ||||||||||| ||||| |   | ||||| ||||| |||||||| ||||||||  ||||||| || |||||||||| ||| ||||| ||| |||| |  || |
-------------------------------------------------gtactgttataat----gacaacttttccagt---tggcaccttacattactggctgt----tccaacatctcgatattt-ttgtaacacaagcgctt--caaattatt----ttcagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAACGTGCTACACTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGGTGGGT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                       || |     || | || ||    |     ||   | || ||  |  |  | |  |    | |    || | | |  | |        ||| | |  |||||  | ||  ||||||||||||||||| | ||||||||| || || |||||||| || |||||  |||| || ||||||||||| ||||||||||| ||||||||||| || |
-------------------------------------------------------ttgatggagcagaaaattttcacgagccgtgacaacaaagatttgtgcctgtgat----actgctaacctagctgatct--------cttgttttgtgtttgactgtggcagGAAGAGAAGGCAATAGGAAGAGGAATACTACCCTTGCTTCAACGAGCTACACTGGTGCAGACATTTGGACAAAGGAATCATGTTTGCTTGAAAGAAGGTT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
gtaagaaattt-agtgtaccgtttta------attttgctattttcatcactat---tagttctattaagaat----tcaaacaaattgtgtggtgtttggtg----agaaggaccttggatt----ttattcttcaatatgtacatggat-attgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
|||||||| || | | |    | | |      | |   | |  |||||   | |   ||||    || |   |    |  ||| || ||       ||| ||     |||  | |||  |  |    |  ||  |   ||    |||   | | | | ||  |  || |  ||||||   |   |  ||||||||||| || |||||||||||||||||||  ||||| |||||||| |||||||||||||| ||||||||  |||||||||| ||||||||||| ||||
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttcatgtccatt-ataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT

upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 2
gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                            ||| | || |   ||  |    ||||    |||  |  || |   || | ||| |   ||  |||   |    |     |   |       ||||  |    |  |||||||||| || |||||| | || ||||| ||||| || || ||||| ||||||||||| || |||||||| ||||| |||||||||||||| ||||| |
------------------------------------------------------------aatgcgaa-atcctgccta-catttgaattgaaaaatattcg---ttgtactttatcttg-gcataactcacatg-tgagtgttccatctttgttcgtattgtgtagGAAGAGAAAGCTATTGAACGGGGGATTCTCCCATTACTCCAACGTGCAACCTTGGTTCAGACTTTTGGACAAAGGAACCATGTGTGCTTGAATGAGGGTT

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|151411015|gb|EV280826.1|EV280826
EST:     ATCATTTCTTTGTGACCCCTCATGACTTTGGGGCATGCTTCCATTATCAA                         GAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACC
genomic: ATCATTTCTTTGTGACCCCTCATGACTTTGGGGCATGCTTCCATTATCAAgtaagaaatt ... tccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                  ttgtaac  putative branch site (score: 2)
                                       tgtttttccgttcc  putative PPT
                               ttttatcatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG