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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcaaatgagattctcttgaatgactaattcttgggtagtgctattctttttttttttttacttgagcattctcaaactcgtgttaatttctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAGGGCCCACAGTTTCTTTTCTTGGATCTGTGCGCTGCTTTCCTTTCACAGC

Basic information

species Glycine max
transcript GLYMA13G05700.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G05700.3 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 10
--tggcaaatgagattctcttgaatgactaattcttgggtagtgctattctttttttttttttacttgagcattctc-aaactcgtgttaatttctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAGGGCCCACAGTTTCTTTTCTTGGATCTGTGCGCTGCTTTCCTTTCACAGC
  |||| ||    || || |||  ||  |  |   |   || |  |||    |  |  |||| | | || | | | | |||    || |  | |     |||||||||||||||||| |||||||| |||||||||||||| || || || ||||||||||| || || ||||||||||| || || ||||||||| | ||||
tatggctaa-atcatactattgcttgtgtcttatataattatt--tataaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC
















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|8403580|gb|BE059214.1|BE059214
EST:     GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
genomic: GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
EST: gi|7028125|gb|AW457908.1|AW457908
EST:     GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
genomic: GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
EST: gi|11688494|gb|BF596170.1|BF596170
EST:     ATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
genomic: ATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
EST: gi|58020231|gb|CX706973.1|CX706973
EST:     TGNAAAATGAAGCTGTTTCTAAGTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAG
genomic: TG-AAAATGAAGCTGTTTCTAAGTCAAATGTGGTCAAGTTTGAAGTGCAGgtaattatcc ... tctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAG
EST: gi|58020051|gb|CX706793.1|CX706793
EST:     TTGAAAATGAAGCTGTTTCTAAGTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAG
genomic: TTGAAAATGAAGCTGTTTCTAAGTCAAATGTGGTCAAGTTTGAAGTGCAGgtaattatcc ... tctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAG
EST: gi|22540977|gb|BU090820.1|BU090820
EST:     GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
genomic: GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
EST: gi|193427695|gb|FK394379.1|FK394379
EST:     CTATAACATGAAGTGCAGATGGGTTGCTGGCAACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAA
genomic: CTATAACATGAAGTGCAGATGGGTTGCTGGC-ACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGG-AA
EST: gi|58019920|gb|CX706662.1|CX706662
EST:     TTGAAAATGAAGCTGTTTCTAAGTCAAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAG
genomic: TTGAAAATGAAGCTGTTTCTAAGTCAAATGTGGTCAAGTTTGAAGTGCAGgtaattatcc ... tctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAG
EST: gi|7028139|gb|AW457922.1|AW457922
EST:     GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
genomic: GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
EST: gi|209725163|gb|BW659833.1|BW659833
EST:     AGTTTGAAGTGCAG                         CTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAG
genomic: AGTTTGAAGTGCAGgtaattatcc ... tctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAG
EST: gi|7234476|gb|AW569813.1|AW569813
EST:     GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
genomic: GAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
EST: gi|254330249|gb|GR841514.1|GR841514
EST:     TTG-AAATG-AGCTGTTTCT-AGTCAAATGT-GTC-AGTTTGAAGTGCAG                         CTTTACAAAACTCGTGA-GAGAAATATCTGCTTGATC-TCAAAGGGTCCAG
genomic: TTGAAAATGAAGCTGTTTCTAAGTCAAATGTGGTCAAGTTTGAAGTGCAGgtaattatcc ... tctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAG
EST: gi|193616494|gb|FK569764.1|FK569764
EST:     AATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT
genomic: AATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCAGATGGGTTGCTGGCACTGCTGGTCATCATGAAGGAATGATTAACAATTCTCTGCATAGTAATCATTACTTTGGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttttttttttttacttgagcattctcaaactcgtgttaatttctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAGGGCCCACAGTTTCTTTTCTTGGATCTGTGCGCTGCTTTCCTTTCACAGC
                                     tgttaat  putative branch site (score: 3)
                                           tttcttt  CT-rich tract
     tttttttttttacttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcaaatgagattctcttgaatgactaattcttgggtagtgctattctttttttttttttacttgagcattctcaaactcgtgttaatttctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAGGGCCCACAGTTTCTTTTCTTGGATCTGTGCGCTGCTTTCCTTTCACAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT