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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattattatttttactcatatctatataaagattgaaatcattattgcttttttttttctttttcggtcactaatcctgattttattttttttttgcagCTCGAAGGAGAGACCCACTCTTGG

Basic information

species Glycine max
transcript GLYMA09G38530.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 2
-ttattattatttttactcatatctatataaagattgaaatcattattgcttttttttttctttttcggtcactaatcctgattttattttttttttgcagCTCGAAGGAGAGACCCACTCTTGG
    ||  |  |     |  |||  |  |     |||   | ||| |    ||||| |||  ||||   | | |     || |||  |||  |||||||||||||||||||||||||||||| ||
tcctttggtgataactgtggtatgaagttttttgttggg-taattctgaaatttttatttaattttgattaattctaagtgttttcttttcatttttgcagCTCGAAGGAGAGACCCACTCTCGG
















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|26045706|gb|CA783207.1|CA783207
EST:     A-TCCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: AGT-CACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|5687979|gb|AI940994.1|AI940994
EST:     GAGTCACAGACTCACCGATCTTCCGATGCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|209717990|gb|BW671821.1|BW671821
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|5057528|gb|AI736004.1|AI736004
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|7284994|gb|AW597481.1|AW597481
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|21286052|gb|BQ473923.1|BQ473923
EST:     GAGTCACAGACTCATCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|16104801|gb|BI892541.1|BI892541
EST:     CAGACTCATCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: CAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|10709482|gb|BF009206.1|BF009206
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|20449584|gb|BQ253708.1|BQ253708
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|120533835|gb|EH261968.1|EH261968
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|6726947|gb|AW311227.1|AW311227
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|7042245|gb|AW472139.1|AW472139
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|120533411|gb|EH261544.1|EH261544
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|16347133|gb|BI972728.1|BI972728
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|6724745|gb|AW309144.1|AW309144
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|16997181|gb|BM086553.1|BM086553
EST:     GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: GAGTCACAGACTCACCGATCTTCCGATTCCCTTTCGTCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG
EST: gi|120533741|gb|EH261874.1|EH261874
EST:     TCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTTGG
genomic: TCTTGGTTTATGAGgtatcttctt ... ttttttgcagCTCGAAGGAGAGACCCACTCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttttttttttctttttcggtcactaatcctgattttattttttttttgcagCTCGAAGGAGAGACCCACTCTTGG
                              tcctgattttattttt  CT-rich tract
                           taatcctgattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattattatttttactcatatctatataaagattgaaatcattattgcttttttttttctttttcggtcactaatcctgattttattttttttttgcagCTCGAAGGAGAGACCCACTCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgatt