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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttgtaatcatttggagaattaccagtttataatttttgttaattactatggtttcttttaattttctaatgttgattccctttgttgaacatgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAAGGGTTTACAGCTCCTCTTTATCGTATAAAG

Basic information

species Glycine max
transcript GLYMA15G10030.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10030.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 13
----------------gtgtgtttgtaatcatttggaga-at-taccagtttataatttttgtt---aattacta--tggtttcttttaattttctaatgttgattccctt-tgttgaacatgca-acagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAAGGGTTTACAGCTCCTCTTTATCGTATAAAG
                |    | |||  |||||| || | || ||    ||||| | |||       |||||| |  ||||    ||| |  || |  | |||  | |    | ||  |  ||   ||||||||| || || || || || |||||||||||||||||| | || |||||||||||||| |||||||| || |||||||| 
gtgaggggttatggcaggaattgtgtgttcattttgatatatatatatatttatcactttcagatagaattacaaattggtgagcttttaccttgttttcttgtctgcaaaatattatatttgtttacagTTGCCTAAAGGGAGGGAAGTTGAGGATGATGACTCATTTATGTTCAATGAAGGGTTTACTGCTCCTCTCTACCGTATAAAA
















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|22523750|gb|BU082561.1|BU082561
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|19934696|gb|BQ079726.1|BQ079726
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|6725094|gb|AW309493.1|AW309493
EST:     AAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: AAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|18734880|gb|BM528438.1|BM528438
EST:     GCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|58020712|gb|CX707454.1|CX707454
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|151404598|gb|EV274412.1|EV274412
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGGGGGATGATGACTCATTTGTTTTTAATGA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGG-ATGATGACTCATTTGTTTTTAATGA
EST: gi|6567265|gb|AW234876.1|AW234876
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|58020885|gb|CX707627.1|CX707627
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|7028742|gb|AW458525.1|AW458525
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATT
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATT
EST: gi|9902981|gb|BE611949.1|BE611949
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTG-TTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|9902896|gb|BE611864.1|BE611864
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|17401651|gb|BM178433.1|BM178433
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|58020543|gb|CX707285.1|CX707285
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|15204199|gb|BI426967.1|BI426967
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|151395410|gb|EV265287.1|EV265287
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
EST: gi|17400275|gb|BM177057.1|BM177057
EST:     GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAG                         TTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA
genomic: GAAGGACTCTGCAATCACTTGCATGTGGAAAAGTTCGTGTCCTACAAAAGgtgtgtttgt ... catgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatggtttcttttaattttctaatgttgattccctttgttgaacatgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAAGGGTTTACAGCTCCTCTTTATCGTATAAAG
       tttcttttaattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtttgtaatcatttggagaattaccagtttataatttttgttaattactatggtttcttttaattttctaatgttgattccctttgttgaacatgcaacagTTGCCAAAGGGTAGAGATGTGGAGGATGATGACTCATTTGTTTTTAATGAAGGGTTTACAGCTCCTCTTTATCGTATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC