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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGCCGCAGAAACTGCTGCAGCTCTTGCAGCTGCTTCTCTGGTTTTTAGAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagccttatgttcattttttggtaattacttttacttggtgcaaattggtcccaactaaatcttaaagagtgtattttgtttctgagtgtag

Basic information

species Glycine max
transcript GLYMA02G01990.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01990.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv07s0005g00740.t01 (Vitis vinifera), 5'ss of exon 3
AGTTGCCGCAGAAACTGCTGCAGCTCTTGCAGCTGCTTCTCTGGTTTTTAGAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagccttatgttc---attttttggta-attacttttacttggtgcaaat--tggt--cccaactaaatcttaaag--agtgtattttgtttctgagtgtag-------------------------------
 || || || |||||||| || |||||||| ||||||||  |||| || |||||||||||||| |||||||||||  || |  |||||||||| || ||||||||  ||||       | ||||   || |  |    |  || ||  |||   ||||  | ||||  |   |||     ||       | |   ||||  | |                               
TGTAGCTGCTGAAACTGCAGCTGCTCTTGCTGCTGCTTCAGTGGTCTTCAGAAGAAGTGACCCTACATACTCCAAGCTTCTCATCAGGAGAGCTATTAGGgtaagatttattccttatacttttaaatacagaaaaaatgttttgtaaaaacaatggtatctcaacacagatttattttcagcccccaatatccttgagacttgatttttttttttttaatctttctgggtacag
















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|192298776|gb|FG988627.1|FG988627
EST:     GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGG                         GTTTTCCAGTTTGCTGATAAGTACAGGG-ATCCTACAGCAATGCCTTGAAA
genomic: GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagcctta ... ctgagtgtagGTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
EST: gi|193640162|gb|FK592715.1|FK592715
EST:     GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGG                         GTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
genomic: GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagcctta ... ctgagtgtagGTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
EST: gi|208293521|gb|GE093481.1|GE093481
EST:     GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGG                         GTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
genomic: GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagcctta ... ctgagtgtagGTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
EST: gi|193719953|gb|FK650449.1|FK650449
EST:     GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGG                         GTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGTAA
genomic: GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagcctta ... ctgagtgtagGTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTG-AA
EST: gi|208058996|gb|GD859000.1|GD859000
EST:     GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGG                         GTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
genomic: GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagcctta ... ctgagtgtagGTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
EST: gi|193547608|gb|FK504569.1|FK504569
EST:     GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGG                         GTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
genomic: GAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagcctta ... ctgagtgtagGTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
EST: gi|193359668|gb|FK323752.1|FK323752
EST:     AAGAAGTGACCCCAACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGG                         GTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA
genomic: AAGAAGTGACCCC-ACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagcctta ... ctgagtgtagGTTTTCCAGTTTGCTGATAAGTACAGGGGATCCTACAGCAATGCCTTGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGCCGCAGAAACTGCTGCAGCTCTTGCAGCTGCTTCTCTGGTTTTTAGAAGAAGTGACCCCACATACTCCAAAATTTTAGTCAGGAGAGCCATCAGGgtaagccttatgttcattttttggtaattacttttacttggtgcaaattggtcccaactaaatcttaaagagtgtattttgtttctgagtgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA