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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggattctagttaattgtttgaagtttgttttgttatgcctggtttgcttagatcttaaattactacaaattctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGTGGCCCTCGGAGATTTCTTGCAGTTTACTTTATCTCTGCAATTGCAA

Basic information

species Glycine max
transcript GLYMA08G19760.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19760.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0034g01410.t01 (Vitis vinifera), 3'ss of exon 4
gtcggattctagt-taattgtttgaagtttgttttgttatgcctggtttgc--ttagatcttaaattactacaaatt---ctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGTGGCCCTCGGAGATTTCTTGCAGTTTACTTTATCTCTGCAATTGCAA
||  | |   ||| | | ||||   | ||| |  | ||||  ||| |||    ||   | ||    |   | | |||   || ||||||| |||||||  || ||||| || ||||||||||| |||||||   ||||||| ||  |||||| |||||||||||| || |  |||||||||||||
gtacgctgtgagtcttactgttgctaatttatcgtcttatagctgatttagagtttcttttttgtctgaaagagatttgcctttgcagGTTAATTGTTTCTCTTTGAATTCTGTTGGTCCTACAGTGGAGAATCTCAGTGGACCAAGGAGATATCTTGCAGTTTATTTCACTTCTGCAATTGCAA
















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|151406516|gb|EV276331.1|EV276331
EST:     GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTG                         GTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
genomic: GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTGgtcggattct ... ttctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
EST: gi|208104251|gb|GD902296.1|GD902296
EST:     GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTG                         GTAAATTGTTATTCCTTGAACTCAG
genomic: GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTGgtcggattct ... ttctctgcagGTAAATTGTTATTCCTTGAACTCAG
EST: gi|22525712|gb|BU084523.1|BU084523
EST:     GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTG                         GTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
genomic: GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTGgtcggattct ... ttctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
EST: gi|9900560|gb|BE609528.1|BE609528
EST:     GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTG                         GTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
genomic: GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTGgtcggattct ... ttctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
EST: gi|58020307|gb|CX707049.1|CX707049
EST:     GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTG                         GTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
genomic: GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTGgtcggattct ... ttctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
EST: gi|58016763|gb|CX703505.1|CX703505
EST:     GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTG                         GTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
genomic: GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTGgtcggattct ... ttctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT
EST: gi|22524413|gb|BU083224.1|BU083224
EST:     GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTG                         GTAAATTGTTATTCCTTGAACTCAGCTGGACCTACTGTGGAGAGCTTCACT
genomic: GGAGACTTGCCACGTCTTCCTTTTTGCATGCCAACATCGGACACCTTTTGgtcggattct ... ttctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttgttatgcctggtttgcttagatcttaaattactacaaattctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGTGGCCCTCGGAGATTTCTTGCAGTTTACTTTATCTCTGCAATTGCAA
                                             ttctctgc  CT-rich tract
                              ttaaattactacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggattctagttaattgtttgaagtttgttttgttatgcctggtttgcttagatcttaaattactacaaattctctgcagGTAAATTGTTATTCCTTGAACTCAGTTGGTCCTACTGTGGAGAGCTTCAGTGGCCCTCGGAGATTTCTTGCAGTTTACTTTATCTCTGCAATTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT