Sequence
atgc intronic sequence ATGC exonic sequencegtgagtccgaaaccctcaccttgtcgttgaatccagaaacaatttccatactacttaatttttcacaagtgttatggttgaacatcatcaacttggtggtgaattggtgatagattggttcacagatttcttaattgagatttcattttttcacaaatgaatgtggcatttttctttggacagCTAAATGAAGCATATGATATGCTAACTTCAAAGAGACCTTGTGGACCAAATAAAAGAGCAATACGTGGCGCTACTTATGATTTGGCTAAGAATGATCCTT
Basic information
species | Glycine max |
transcript | GLYMA04G39890.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39890.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g02120.2 (Oryza sativa), 3'ss of exon 5
gtgagtccgaaaccctcaccttgtcgttgaatccagaaacaatttccatactacttaatttttcacaagtgttatggttgaacatcatcaacttggtggtgaattggtgatagattggttcacagatttcttaattgagatttcattttttcacaaatgaatgtggcatttttctttggacagCTAAATGAAGCATATGATATGCTAACTTCAAAGAGACCTTGTGGACCAAATAAAAGAGCAATACGTGGCGCTACTTATGATTTGGCTAAGAATGATCCTT
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-------------------------------------------------------------------------------------------gtaggtttcatcttcttgaattcttaacttgtcagggttataagccaggccacattctt---------agcatttatcttttgcttg--cagCTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAATAAGAGAGCGATCCGTGCTGCAACTTATGATCTTGCTAAGAATGATCCAC
upper sequence: GLYMA04G39890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g02510.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtccgaaaccctcaccttgtcgttgaatccagaaacaatttccatactacttaatttttcacaagtgttatggttgaacatcatcaacttggtggtgaattggtgat--agattggttcacagatttc--ttaattgagatttc---attttttcacaa-atgaatgtggcatttttctttggacagCTAAATGAAGCATATGATATGCTAACTTCAAAGAGACCTTGTGGACCAAATAAAAGAGCAATACGTGGCGCTACTTATGATTTGGCTAAGAATGATCCTT
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-----------------------------------------------------------------------------------------gtcttgg-attaattcagtcatggagattactttctaaattacatttgattagaactttggaaaagttttatagtactgttgtggcatgtca-tttgggcagCTGAATACAGCCTATGATACGCTTACTTCAAAGAGACCGTGCGGACCCAGTAAACAAGCAATACGTGGAGCTACTTACGATCTAGCTAAAAATGACCCATMapped 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|192306513|gb|FG997211.1|FG997211EST: GAGCTCCAGCGGTGGCAATTGCTTATTTGTTCTGGTTTTGTGACATGAAT CTAAATGAAGCATATGATATGCTAACTTCAAAGAGACCTTGTGGACCAAAT
genomic: GAGCTCCAGCGGTGGCAATTGCTTATTTGTTCTGGTTTTGTGACATGAATgtgagtccga ... ctttggacagCTAAATGAAGCATATGATATGCTAACTTCAAAGAGACCTTGTGGACCAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttaattgagatttcattttttcacaaatgaatgtggcatttttctttggacagCTAAATGAAGCATATGATATGCTAACTTCAAAGAGACCTTGTGGACCAAATAAAAGAGCAATACGTGGCGCTACTTATGATTTGGCTAAGAATGATCCTT
tcttaat putative branch site (score: 3)
catttttcttt putative PPT
agatttcatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtccgaaaccctcaccttgtcgttgaatccagaaacaatttccatactacttaatttttcacaagtgttatggttgaacatcatcaacttggtggtgaattggtgatagattggttcacagatttcttaattgagatttcattttttcacaaatgaatgtggcatttttctttggacagCTAAATGAAGCATATGATATGCTAACTTCAAAGAGACCTTGTGGACCAAATAAAAGAGCAATACGTGGCGCTACTTATGATTTGGCTAAGAATGATCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA