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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttagttaattggttactatagtatcatcttcccttccctttccaatctaaatctcttctcgtgttattatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAG

Basic information

species Glycine max
transcript GLYMA14G00500.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G00500.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 2
gttagttagttaattggttactatagtatcatcttcccttccctttccaatctaaatctctt-ctcgtgttattatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAG
|| | |  |||  |  |    | | |   | |   |      | ||| | | |   |   || || || |     |  |||||||| |||||||||||||| ||||||||||| || || || ||||| ||||| || || ||||| |||||||| ||||
gtaaat--gtttttcagcacttgttgatgcttgggctagcttccttctattttggtttatttacttgtatctgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAG
















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|22928993|gb|BU546132.1|BU546132
EST:     ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATG                         GTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
genomic: ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATGgttagttagt ... attatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
EST: gi|7924578|gb|AW830604.1|AW830604
EST:     ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATG                         GTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
genomic: ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATGgttagttagt ... attatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
EST: gi|298199186|gb|HO042549.1|HO042549
EST:     ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATG                         GTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
genomic: ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATGgttagttagt ... attatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
EST: gi|24205490|gb|BU964743.1|BU964743
EST:     ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATG                         GTGACTCCTAATCTCTATGGAAATCTAGTGGCTA
genomic: ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATGgttagttagt ... attatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTA
EST: gi|193612976|gb|FK565079.1|FK565079
EST:     ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATG                         GTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
genomic: ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATGgttagttagt ... attatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
EST: gi|22927386|gb|BU544525.1|BU544525
EST:     ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATG                         GTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
genomic: ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATGgttagttagt ... attatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
EST: gi|208163744|gb|GD963272.1|GD963272
EST:     ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATG                         GTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT
genomic: ATAATTGCTGCATGCAACTTGTCTCCAAACCAGAGCAGTTCGATGTTATGgttagttagt ... attatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcatcttcccttccctttccaatctaaatctcttctcgtgttattatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAG
                        atctaaa  putative branch site (score: 3)
                                              ttatctc  putative PPT
                       aatctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttagttaattggttactatagtatcatcttcccttccctttccaatctaaatctcttctcgtgttattatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA