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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatatgctagtaattcttgttttgttcttaaattgctctattgacctagcaatttcctttcctactcttataactaaaaacaaattatacaatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAGACTATTTGAACCAATCTATGA

Basic information

species Glycine max
transcript GLYMA18G53700.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G53700.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 3
gaatatgctagtaatt--------cttgtt-ttgttcttaaattgctctattgacctagcaatttcctttcctac---------tcttata-actaaaaacaaattatacaatcatg--caGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAGACTATTTGAACCAATCTATGA-
| || |  | || |||        |||||  |||||   ||  |||| |    || |   | ||    ||  ||          ||| |||   |||    | |    |||  ||     |||  ||||||| || | || || |||||||||||||| |||||||||||||| ||||||||||| || ||||| |||| ||| ||||| ||||||||||| 
gtatctttttgtgattgtcttagacttgtggttgttaacaacatgctattaaaactttagagttcttctttatatgaaaagttgtctgatatgttaatggtatacctgacatgcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGTGGTGAAGGATATTCAGGATGCCTGCAAACTTTTTGAGCCAATCTATGAC

upper sequence: GLYMA18G53700.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 3
gaatatgctagtaattcttgttttgtt---cttaaattgctctattgacctagcaatt--tcctttcctactcttataactaaaaac--aaattatacaatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAGACTATTTGAACCAATCTATGA-
        |||| |||||  | |||     | |  | | |  || | || |   | ||  |||||      |  || | |||| |    |||   |   ||  |||||||||||||| | | |||| |||||||||||||||||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||||||||| 
--------tagttattctgctcttgcaggacctggaatccaatactaacatccgagttgatccttcagagttggtaaatctaacattttaaacctttggattctgcagGGAACTTGTACTAGCAGGAAAAGACATTGAAAGTGCATACTGGGAGCTTGTGGTGAAGGACATCCAAGATGCGTGCAGACTTTTTGAGCCAATCTATGAT
















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|7233907|gb|AW569249.1|AW569249
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|6566822|gb|AW234454.1|AW234454
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|12689429|gb|BG155826.1|BG155826
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|213592579|gb|DB961839.1|DB961839
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|213593697|gb|DB971719.1|DB971719
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|7233788|gb|AW569131.1|AW569131
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|21887135|gb|BQ740348.1|BQ740348
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|298196531|gb|HO041274.1|HO041274
EST:     CATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: CATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|254318817|gb|GR830381.1|GR830381
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|6913943|gb|AW395473.1|AW395473
EST:     GATCTGTGAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGGTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGCGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|18721154|gb|BM523327.1|BM523327
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|298174178|gb|HO017514.1|HO017514
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAGTGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|7924409|gb|AW830435.1|AW830435
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         CGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
EST: gi|24136489|gb|BU926999.1|BU926999
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAG
EST: gi|24205422|gb|BU964675.1|BU964675
EST:     GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA                         GGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG
genomic: GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAggtaccatca ... caatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctagcaatttcctttcctactcttataactaaaaacaaattatacaatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAGACTATTTGAACCAATCTATGA
                           aactaaa  putative branch site (score: 2)
                       ttataactaaaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatatgctagtaattcttgttttgttcttaaattgctctattgacctagcaatttcctttcctactcttataactaaaaacaaattatacaatcatgcaGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAGACTATTTGAACCAATCTATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- -tatgcta
- - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - -cctagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa