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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtgtgcaagttcctttaatcttgtttctagtgctgttctgtggttatgattaatctatggtgaaattacagcaattctttctcacgtgtctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG

Basic information

species Glycine max
transcript GLYMA03G35480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g05900.1 (Oryza sativa), 3'ss of exon 4
gtgtgtgcaagttcctttaatcttgtttctagtgctgttctgtggttatgattaatctatggtgaaattacagcaattctttctcacgtgtctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG
                      | || | |  | || ||  |    |   | | || | |  | |  |     | |    || ||||   | |  | |||||||||||||| ||||||||  ||||||||||||||||||| ||||||||||| ||||  ||  |    || || || |  || ||||| || |||  | 
---------------------gtagtgtgttatcctattgcgatcatggtactgatatttcattaggtggattctaactgttgtcacacatgtaatgcagATGGCAGATCCCTTGACTGCATTGATGTATGCAGTACAAGTGATGAATTTTCTTAAGATGCTAATACAAAAAACCCTCAAGGATAGAGAAGAGTCTGATC

upper sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g05540.1 (Oryza sativa), 3'ss of exon 4
gtgtgtgcaagttcctttaatcttgtttctagtgctgttctgtggttatgattaatctatggtg--aaattacagcaattctttct------cacgtgtctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG
                               ||  ||  ||||  | || || ||  |||| |   || |     | || ||| ||      ||| | | |  | |||||| ||||||| ||||| || ||||||||||| || ||||| ||||||||||||||||  ||  |   |||||| || |  |  ||| | || || | | 
-------------------------------gtaatgcactgtcctaataataaacttatgattttaagtgtggtcgatgcttactgtcatgcacatatgtaatgcagATGTCAGATCCATTGACCGCACTGATGTATGCGGTGCAAGTGATGAATTTTCTCAAGATGCTAATACAGAAGACCCTCAAGGGTAGACAAGAGTCCAATC

upper sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
gtgtgtgcaagttcctttaatcttgtttctagt-gctgttctgtggt-tatgattaatct---atggtgaaa---ttaca---gcaattctttctcacgtgtctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG
|| | ||||  ||    |||| ||||  | | | ||      |   | |||   | | |       ||| ||   |||     || |    ||  ||    |    | ||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||  || ||    ||||| || |  || |||||||| || | | 
gtat-tgca--ttgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC

upper sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G113073_T01 (Zea mays), 3'ss of exon 4
gtgtgtgcaagttcctttaatcttgtttctagtgctgttctgtggttatgattaatctatggtgaaattacagcaattctttctcacgtgtctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG
|| | ||||  ||    | ||    |  | | |      || |   |||                ||| |    ||  || |  ||||  |    | ||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||  || ||    ||||| || |  || |||||||| || |   
gtat-tgca--ttgtgctgatacgatagcgattagcaaactatcaatatatacttcacccatcacaatgatgctaa--ctatagcacgcttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCGACCC

upper sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g03140.t01 (Vitis vinifera), 3'ss of exon 4
--gtgtgtgcaagttcctttaatcttgtttctagtgctgttctgtggttatgattaatctatggtgaaattacagcaattctttctcacgtgtctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG
       |  || |    | | |  ||||| |  |  | |  | | ||| ||  ||   | |||| ||  |   |        | ||   |||    | |||||||||||||| ||||| ||  ||||||||||||| ||||| |||||||||||||||||| |  |  | | ||| || || ||||| ||||| || || |
atcctcttttaaataaactcactgatgtttttcttattttgatatagttttg--tacattctggtcaatgtgaggtgcaatgatatcttctgttggttgcagATGGCAGATCCCTTGACAGCCTTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGACTTTGATAATCAGGACGCTTAGGGAAAGGGAGGACTCAATAG

upper sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------gtgtgtgcaagttcctttaatcttgtttctagtgc---tgttctgtggttatgat---taatctatggtgaaat-tacagcaattctttctcacgtgtc----tcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG-
                                                                                    ||| | | |  |    |   ||   ||  |  |    | ||| ||| ||||| |   | |  | | ||  ||| |  | || || ||      |  ||    |||| |||||||| |||||  |||| ||||||||| |||| || ||||||||||| || ||||| |||||  |  |    |||||||  ||  || |||   || ||| 
gtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagatttcactacagatgctgtcttcgacgtttcatgtgctgaatttgaacgtaggtattccgtgtttatggtgtttcaattgttgtagaatgtgtaacatttattgacattgcttcattatccttcagATGGCTGATCCACTGACAGCTCTGATGCATGCTGTTCAAGTCATGAACTTGCTCAAAACTCTGATTCTTCGCACACTGAAGGACCGAAAGGCCACT-TTGC

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|22521721|gb|BU080532.1|BU080532
EST:     AGATGAATGCACGCAATATTGCAATGGTTTTTGCTCCAAACATGACTCAA                         ATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTT
genomic: AGATGAATGCACGCAATATTGCAATGGTTTTTGCTCCAAACATGACTCAAgtaagagtaa ... tctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgattaatctatggtgaaattacagcaattctttctcacgtgtctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG
                                   ttctcac  putative branch site (score: 2)
                                           tgtctcct  CT-rich tract
     attaatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgcaagttcctttaatcttgtttctagtgctgttctgtggttatgattaatctatggtgaaattacagcaattctttctcacgtgtctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
gtgtgtg
- - - - - gttcctt
- - - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - -ctgtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatggtg