Sequence
atgc intronic sequence ATGC exonic sequence...tttatgtggcatctttgttttttttttttttttcttttaatatgcttgcatttccattttgtgttaacgattggtgattttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG
Basic information
species | Glycine max |
transcript | GLYMA07G35750.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g38800.1 (Oryza sativa), 3'ss of exon 2
---------tttatgtggcatctttgttttttttttttttttcttttaatatgcttgcatttccattttgtgttaacgattggtgattttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG
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tgtccttggcttgtataccatatgagaaagtacttgtatgttttatctatgtaattattttgtattctggaattgacaatt--ttactttct-------tcatgtacagTATGCTCATAGAGCTTGTGTGCAACGCTGGTGCAATGAGAAAGGAGACATTACATGTGAAATCTGTCATGAG
upper sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
tttatgtggcatcttt--gttttttttttttttttcttttaatatgcttgcatttccattttgtgttaacgattggtgattttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG
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-tgattgaatctgttaaggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagat-tttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
upper sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G118957_T04 (Zea mays), 3'ss of exon 3
-tttatgtggcatctttgttttttttttttttttcttttaatatgcttgcatttccattttgtgttaacgattggtgattttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG
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gtctaactgcttacctaagtttgtcttttgccatcctgtacgagccaagcattgcataaatctgtttgctaattttt-ttataccacatttgtttgcacagTATGCTCACAGGGAATGTGTGCAACGTTGGTGCAATGAGAAAGGAGATATAATCTGTGAAATCTGCCATGAG
upper sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 1
lower sequence: AT2G02960.4 (Arabidopsis thaliana), 3'ss of exon 2
-----tttatgtggcatctttgttttttttttttttttcttttaatatgcttgcatttccattttgtgttaacgattggtga----ttttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG
||| | | || || ||| | || | || || | | | | | || || ||| ||||||| | || ||| ||||||||||||||||| || |||||||||||||||||||| || ||| |||| || || ||||| ||||| ||
gttagttttcatcatcatctaattcttaaaccatttggtctatattgagcaatggctttgttctagaataattgactgttgacgaattttttgttatgtttttgaccagTATGCTCATAGAAAATGTGTTCAGCGTTGGTGCAATGAAAAGGGAAACATTATATGCGAGATTTGTCACCAG
upper sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 4
tttatgtggcatctttgttttttttttttttttcttttaatatgcttgcatttccattttgtgttaac--gattggtgattttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG
| | | | | || | ||| | || |||| || | | | ||| | ||| || ||| || | |||| | |||||||||||||| ||||| ||||| || ||||||||||||||||||||||||||||||||||| || ||| ||
--tgtattgtcattatgagataaaatttagtactccttgatatttttctctctaactccattgtcagtcaaatttgttattgactgtatattttttttccagTATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcatttccattttgtgttaacgattggtgattttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG
tgttaac putative branch site (score: 2)
attttttggaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatgtggcatctttgttttttttttttttttcttttaatatgcttgcatttccattttgtgttaacgattggtgattttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- -atgtggc
- - - - - - - - - - - - - - - - - - - - - -gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attggtg