Sequence
atgc intronic sequence ATGC exonic sequence...atatatgccattaaatttttttttttcagtagaaaataaaattggatttaatagatgaataatgatacttattcattgttaagcagatctcgtcattcagGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTGTGGCGTGGATACAA
Basic information
species | Glycine max |
transcript | GLYMA05G04340.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G04340.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------atatatgccatta-aattttttttttt-------cagtagaaaataaaa---------ttggatttaatagatgaataatgatacttattcattgttaagcagatctcgtcattcagGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTGTGGCGTGGATACAA
|||| || | | || ||| |||||| || |||||| ||| || |||| | || ||| | | || | || ||||| | || || ||||| || |||||||| || |||||| |||||||||||||||| |||||||||| || ||| |||| || ||||| | | || | |
gtaagttttctttttctagtttgatgatatttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG--------------
upper sequence: GLYMA05G04340.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22540.2 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------atatatgccatta-aattttttttttt-------cagtagaaaataaaa---------ttggatttaatagatgaataatgatacttattcattgttaagcagatctcgtcattcagGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTGTGGCGTGGATACAA
|||| || | | || ||| |||||| || |||||| ||| || |||| | || ||| | | || | || ||||| | || || ||||| || |||||||| || |||||| |||||||||||||||| |||||||||| || ||| |||| || ||||| | | ||
gtaagttttctttttctagtttgatgatatttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagCAGGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATA-----------------
upper sequence: GLYMA05G04340.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 1
-----atatatgccattaaatttttttttttcagtagaaaataaaa---------ttggatttaatagatgaataatgatacttattcattgttaagcagatctcgtcattcagGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTGTGGCGTGGATACAA
| | || |||| |||| || |||||| ||| || |||| | || ||| | | || | || ||||| | || || ||||| || |||||||| || |||||| |||||||||||||||| |||||||||| || ||| |||| || ||||| | | || | |
tttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG-------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttaatagatgaataatgatacttattcattgttaagcagatctcgtcattcagGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTGTGGCGTGGATACAA
atttaat putative branch site (score: 4)
tctcgtc putative PPT
aataatgatacttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatatgccattaaatttttttttttcagtagaaaataaaattggatttaatagatgaataatgatacttattcattgttaagcagatctcgtcattcagGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTGTGGCGTGGATACAA
- -tatgcca
- - - - - - - - - - - - - - - - aaaataa