Sequence
atgc intronic sequence ATGC exonic sequence...ttgttactgattatgaatgttctaatgctagataggcattccaatttctttatatagatctattctaaaaattttaaggtactgatggttgccttttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT
Basic information
| species | Glycine max |
| transcript | GLYMA13G37090.1 |
| intron # | 21 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os04g28460.1 (Oryza sativa), 3'ss of exon 17
-------------------ttgttactgattatgaatgttctaatgctagataggcattccaatttctttatatagatctattctaaaaattttaaggtactgatg-gttgccttttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT--------------------------------------------------------------------------
| | | ||| |||| | | |||| | | ||| | | | || | | | | || | |||| | ||| ||||| || ||||| ||||| |||||||||||||| | ||||| || |||| ||||||| ||||||||||||||||| ||| ||||||| |
gtgagtctcttgattctaatcctctttagttaggaatatcttt-tgctgtactgagcttctgctactgctttgcttttcccaccgccacctgtcaa--tgctgacctagcactcttttagtttctcctttatatcaggactctctggaactagcttgttcaactcaattagtctgatggcctataatgttttctatacaagTCTTCCTGTGACGACTATAATTTTTGACAAGGATATCTCTGAGGAAACAGTACTGCAATATCCCCAGATTTTACTCTATTCTCAGTCTGGAAG
upper sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 21
------------------------ttgttactgattatgaatgttctaatgctagataggcattccaatttctttat--atagatctattctaaaaat---tttaaggtactgatggttgcctttt-------cagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT
|| || || ||| ||| | | |||||| |||| | || | ||||| || | || || | || || || ||| | | |||| ||||||||| ||| |||| ||| | ||||||| || || ||||| || ||||| |||||||||||||| || ||||| || || ||||||||||| | |
gtaagtcaaacttagtctggcatctttttgcttatt-tgagt-tcttaatgc--aatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAGTTTGATGGCTTATAACGTCTTCTACACAAGCATTCCTGTTCTAACTACT
upper sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G479163_T01 (Zea mays), 3'ss of exon 3
ttgttactgattatgaatgttctaatgctagataggcattccaatttctttatatagatctattctaaaaattttaaggtactgatggt-tgccttttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT
|| || || | || | | || ||||| | | | ||| | || | | || || | || | ||||||||| ||| ||||||| | ||||||| ||| | ||||| || ||||| ||||||||||||||||||||||| || || |||||||| || | |
-----gtaagccataaaccgtccgtacttgtattatggt----agttggacgtatag-tgtgtgctagttttcttgat-tgctcatattctgtgcatgcagTTTTTCTTTTCTTTCAGGCATTGCTGGAACAAGCTTATTCAACTCAGTTAGTTTGATGGCTTATAATGTTTTCTACACAAGCATTCCTGTTTTAACTACT
upper sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G037335_T01 (Zea mays), 3'ss of exon 7
----------------ttgttactgattatgaatgt-tctaatgctagataggcattccaatttctttatatagatctattctaaaaattttaaggtactgatggttgccttttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT
|| | || || || | | || | || | | ||| | || || | | | | | || | || ||| || ||| | ||| | || || | ||||| |||||| | ||||| || ||||||||||||||||||| ||||||||||| ||| | || || | |
gtgagttttccttgtaatgcttatgccattggctgcatttttcattacaagcttatgctactttgcactttggcatgggttttgtgggtgcaactgctcacttgagtccccttttagGTTTGCCTTTTTGTCGGGGCTATCTGGGACTAGCTTATTCAACTCAATTAGCTTGATGGCTTATAACGTTTTCTATACAAGTTTACCCGTCATGACTATA
upper sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 20
ttgttactgattatgaatgttctaatgctagataggcattccaatttctttatatagatctattctaaaaattt-taaggtactgatggttg--ccttttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT
| | | || | || ||||| | |||| || | ||| |||| | || | | |||||| | || | || || || ||||||||||| || |||||||| || || |||||||| |||||| ||||||||||||| |||||||| || |||||||||||||| || |||
------------gtaagt-ttattatctcagatatg---------ttctcagtagatatc-attcaagtcgttcatgaaatactgacaacagaatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttatatagatctattctaaaaattttaaggtactgatggttgccttttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT
tactgat putative branch site (score: 2)
ttgccttttc putative PPT
tatatagatctattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttactgattatgaatgttctaatgctagataggcattccaatttctttatatagatctattctaaaaattttaaggtactgatggttgccttttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT
- gttactg
- - - - - - -tgaatgt
- - - - - - - - - - -ctaatgc
- - - - - - - - - - - - - - - - - -gcattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg
