Sequence
atgc intronic sequence ATGC exonic sequence...aatactgcactttatttcatgttatttttacatgaattgaagttaaaatgatggatacaattcaatctctgagtaatttgtattctatttaaatgtcaagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCG
Basic information
species | Glycine max |
transcript | GLYMA03G27580.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G27580.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
------aata--ctgcactttatttcatgtt-atttttacatgaattgaagttaaaatgatggatacaattcaatctctgagtaatttgtattctatttaaatgtcaagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCG
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ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtggaacttaatgttatc-atctatttta--ttcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT------
upper sequence: GLYMA03G27580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 2
aatactgcactttatttcatgttattt----ttacatgaattgaagttaaaatgatggatacaattcaatctctgagtaatttgtattctatttaaatgtcaagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCG
|| | || ||| | | | | | | ||||| || || | ||| || ||||| | ||| || | ||| | | ||| ||||| | ||||||||| ||||||| |||||| ||||||||| ||||||||||||| | |||||||||||||| | | ||||||||||
-attattcaaattactgtacaatctctggattcttatgaacaatgagtagaaagttgggtataattctttgctcttctaagtttttggatatgatgagcagGACAAGATGATGGAAGTGGTAGGTCAAAGCAGAGCAGAAGTGAAAAGAAGTCTCGCAAGGCAATGTTGAAACTTGGAATGAAGACAATTCCAGGTGTCAG---
upper sequence: GLYMA03G27580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
aatactgcacttta---------tttcatgttatttttacatgaattgaagttaaaatgatggatacaattcaatctctgagtaatttgtattctatttaaatgt-caagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCG
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-gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG---------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|7692485|gb|AW760590.1|AW760590EST: ATGAGGATGACGAAGATGACGACGATGAGGATGACGACAATGTT---G AAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTC
genomic: ATGAGGATGACGAAGATGACGACGATGAGGATGACGACAATGTTGAAGgtaaattggc ... aaatgtcaagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTC
EST:
gi|193345380|gb|FK312959.1|FK312959EST: TGATGAGGATGACGAAGATGACGACGATGAGGATGACGACAATGTTGAAG AAGGTGATGTATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTC
genomic: TGATGAGGATGACGAAGATGACGACGATGAGGATGACGACAATGTTGAAGgtaaattggc ... aaatgtcaagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgatggatacaattcaatctctgagtaatttgtattctatttaaatgtcaagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCG
agtaatttgtattcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatactgcactttatttcatgttatttttacatgaattgaagttaaaatgatggatacaattcaatctctgagtaatttgtattctatttaaatgtcaagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCG
- - -tgcactt
- - - - - - - - tcatgtt
- - - - - - - - - - - - - - - catgaat
- - - - - - - - - - - - - - - - - - - - - - - -atgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caattca