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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcactttcttttataagctgagtctggagtagttgtgttacttgtgtagctaatcatttgtcttcacttcactcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAA

Basic information

species Glycine max
transcript GLYMA10G06580.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 4
gtatgcact--ttcttttataagctgagtctggagtagttgtgttacttgtgtagctaatcatttgt---cttcacttcact-cataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAA
||| || ||   ||   || || |     |  ||| |        || ||| ||  || |  ||||    ||  |   || | | |  ||||||||||||||| | || ||||| |||||||| || |||||||| |||||||| || ||||| |||||||||||||||||      |   | |||||| |
gtaagctctgaatccactaaaaccatgagcaagagcaacaaaa--acctgtatatatacttgtttgcttactgtatgccattgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTA

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 4
----------------------gtatgcactttcttttataagctgagtctggagtagttgtgttacttgtgtagctaatcatttgtcttcacttcactcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TAGATGGTGTAA
                      |   ||| | | || | || |      | | |||   |   |   |       ||  | |||  | ||      | | ||  ||||||||||| ||    || ||||| |||||||| || |||||||| || |||||||| || || |||||||||||||| | | | |||    | |||||| |
gtaagttcaaaaaatactgagtgctagcattatgttctttatgt--gcccagaagttactac-tagatcacaacactcttgattattattattaatatttattgcagTGGATGCTCCAGATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTA

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
----------------------gtatgcactttcttttataagctgagtctggagtagttgtgttacttgtgtagctaatcatttgtcttcacttcactcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TAGATGGTGTAA--
                      |   ||| | | || | || |      | | |||   |   |   |       ||  | |||  | ||      | | ||  ||||||||||| ||    || ||||| |||||||| || |||||||| || |||||||| || || |||||||||||||| | | | |||    | |||||| |  
gtaagttcaaaaaatactgagtgctagcattatgttctttatgt--gcccagaagttactac-tagatcacaacactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTAAT

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 4
--------gtatgcactttctt--ttataagctgagtctggagtagttgtgttacttgtgtagcta-atca-tttgtc---ttcacttcactcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAA
        |   || |||| |   |  |   ||   || ||      |    | | | ||||| || |||| |||||      ||  ||| |  |  ||||||||||||||| | || ||||| |||||||| || || ||||| ||||||||||| ||||| ||||| |||||||| ||   |  |   |  || || |
tatccacggcgagctctttatcaatattccactccttcaggtccctcttcactgcctctgtagttacatcaatttgttgatgacatgtcattgttttcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGAAAGGACAAGTTTGGTGAGGAAATGAAGAAAAACGCTCAAGCTGCAGGAGTTA

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 4
--------------gtatgcactttcttttataagctgagtctggagtagttgtgttacttgtgta-gctaatcatttgtcttcacttcactcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAA
                |    | || | | ||   || |  |  ||  |           |   ||    | |    || |  ||  ||  |  |  ||||||||||||||| | || ||||| |||||||| || || ||||| || |||||||| ||||| |||||||||||||| ||   |  |   |  || || |
aaactgcatcatcgaaacaggccttttataatctactaaaccgtgaacaaccaaaaactgtagttacatcagtttgatgacggcatgtccttgttttcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGGAAGGACAAGTTTGGTGAGGAGATGAAGAAAAATGCTCAAGCTGCAGGAGTTA

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G089767_T01 (Zea mays), 3'ss of exon 2
----------------------------gtatgcactttcttttataagctgagtctggagtagttgtgtta---cttgtgtagctaat---catttgtcttcacttcactcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TAGATGGTGTAA
                             |    |  |  |    || |   ||||  || | |||   | |   | |  | |  |||     |    || | || | |||  |  |||||||||||||||   || |||||  ||||||| || |||||||| || ||||| || ||||| ||||||||||| || ||||| |||    | |||| | |
gtaagctctgaagaaaaaccacaataatattcaaagctattagcctatgaccagtcctgattggttacataaactcataagaaattaaaacataacaatcctgacattactttt--cagTGGATGCTTCAAATTCCTGGTGCATCAAGTTACATTGGTTGCATCGGGAAGGATAAGTTTGGTGAGGAGATGAAAAA-AAATGCACAAGCTGCTGGTATTA

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
--gtatgcactttcttttat-aagctgagtctggagtagt-tgtgttacttgtgtagcta-atcatttgtcttcacttcactcata--------acagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAA
    ||  | | | |  |||  |||| ||  |   |  || | |  || ||  | |  |  ||   || |||   |||  ||  |          |||||||||||||||   || || || ||||| ||||| || ||||| ||||||||||| ||||| ||||| |||||||| || |  | ||| | |||||| |
gtacataaaatatttactattgagcttagctttccgctgtattttctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 4
--gtatgcactttcttttat-aagctgagtctggagtagt-tgtgttacttgtgtagct--aatcatttgt---cttcacttcactcata----acagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAA
    ||  | | | |  |||  |||| ||  |  |   || | |  || ||  | |  |  | ||||||     | |  | |      |      |||||||||||||||   || || || ||||| ||||| || ||||| ||||||||||| ||||| ||||| |||||||| || |  | ||| | |||||| |
gtacataaaatatttactattgagcttagctttcatctgtattttctaattaagaaatttcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA

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|8284137|gb|BE021696.1|BE021696
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|6454402|gb|AW185085.1|AW185085
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|213618065|gb|DB963698.1|DB963698
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|17022031|gb|BM093065.1|BM093065
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|209709321|gb|BW680986.1|BW680986
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGANAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|12690012|gb|BG156348.1|BG156348
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|151394548|gb|EV264419.1|EV264419
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|5606299|gb|AI900405.1|AI900405
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|120531830|gb|EH259963.1|EH259963
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|19936079|gb|BQ080713.1|BQ080713
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
EST: gi|13125032|gb|BG315575.1|BG315575
EST:     GTGCTACTCACAATTCAATCAGGGTTGCTCAG                         TGGATGCTTAAAGCACCAGGTGCCACAAGTTATATA
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATA
EST: gi|16105072|gb|BI892812.1|BI892812
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ctcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtagttgtgttacttgtgtagctaatcatttgtcttcacttcactcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAA
                     agctaat  putative branch site (score: 3)
                                  tcttcacttcactc  putative PPT
                        taatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcactttcttttataagctgagtctggagtagttgtgttacttgtgtagctaatcatttgtcttcacttcactcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA