Sequence
atgc intronic sequence ATGC exonic sequence...ttatgtgggtaatgaattttaatctactattgcttattgttggtggccatttcttctgaaatttaagactgataatttttacacttgctgcctgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
Basic information
| species | Glycine max |
| transcript | GLYMA02G03800.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 5
ttatgtgggtaatgaattttaatctactattgcttattgttggtggccatttcttctgaaatttaagactgataatttttac------acttgc-tgcctgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
|| | || ||||| | || || | || |||||| | | | | | | | | | ||| || || || | |||| | | || |||| || || || |||||||||||||| ||||| ||||| |||||||||||||||||| | || |||||| |||| |||| || | |||| |||||||
---gttgaattattc-ttttagtaaaccat-gttttttgttga-agtcttctttcccgcagctgtgctctg-tatcttatatcgaattatttgcattgcatttccagGTTGCAACAAAAACTGAGTCAAATAAGAACGCAGGAAATGCTATTTTATATGAATGTGTTGAGACTATAATGGGCATCGAAGCTACTAGTGGTTTACGTG
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G030144_T01 (Zea mays), 3'ss of exon 5
ttatgtgggtaatgaattttaatctactatt--gcttattgttggtggccatttcttctgaaatttaagactgataatttttacacttgctgcctgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
| || || || | ||| || | |||| ||| || || | || ||| || ||| | | | || |||| | ||||| || ||||||||||| ||| || ||||| ||||||||||||||||| | ||||||||||||||||||| || |||| |||||||
-atcatcattatcttatctttgtacactttttgggttatctttgcacttggcatcccctttatctttgtgtggattatgaacacatgaatttctt-ttccagGTTTCAACGAAAACCGAGTCAAATAAGAATGCTGGAAATGCTATTTTATATGAATGTGTGGAGACAATAATGAGCATTGAAGCTACAAGTGGTTTACGTG
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G017421_T02 (Zea mays), 3'ss of exon 5
----ttatgtgggtaatgaattttaatctactattgcttattgttggtggccatttcttctgaaatttaagactgataatttttacacttgctgcctgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
|||| | ||| | || || ||| | | | |||| | | || | || | ||| || |||| | | | || |||| | || || |||||||||||||| ||| || ||||| |||||||||||||| || | ||||||||| ||||||||| || |||| |||||||
catcttatctttgtagt---ttgtactcttttttgggttatcttcacacttggcattccctttatctttgcatggattataaacacacgaatttctt-ttccagGTTTCAACAAAAACTGAGTCAAATAAGAATGCTGGAAATGCTATTTTATATGAATGCGTGGAGACAATAATGGGCATTGAAGCTACAAGTGGTTTACGTG
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 5
ttatgtgggtaatgaattttaatctactattgcttattgttggtggccatttcttctgaaatttaagactgataatttttacacttgctgcc--tgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
| |||| | | ||| || || ||| | | || || || | | | | | | ||| || | | ||| ||||||||| | || || |||||||| ||| |||||||||||| || |||| ||||| |||||||| ||||||||||| ||||| ||||||||| |||| |
-tttgtgaa-atttgctttgaaaacgcttttgatctacatcagtcaggatcgtaattgcagataatcatttttgattcctaagttgatttttaatgtattagGTGGCATCAAAAACCGAGTCAAACAAAAATGCAGGGAATGCTATCCTATACGAATGCGTTCAAACGATAATGAGCATCGAAGAAAATGGTGGCCTACGAG
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
ttatgtgggtaatgaattttaatctactattgcttattgttggtggccatttcttctgaaatttaagactgataatttttacacttgctgc----ctgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
| |||| | || | | || ||| | | | | | || || |||| | ||| || |||| | || || |||||||| || || ||||||||||| ||| ||| |||||||||||||| |||||||||||| |||| || |||||||||||||||| | ||||||||||||
-tttgtgcatgctg--ctattatttacc-tagaaaaaaatacgctgcataaatggacaaagtttacttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccatttcttctgaaatttaagactgataatttttacacttgctgcctgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
gactgat putative branch site (score: 3)
cctgtttt putative PPT
aaatttaagactgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgtgggtaatgaattttaatctactattgcttattgttggtggccatttcttctgaaatttaagactgataatttttacacttgctgcctgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- -tgtgggt
- - - - - - - - - - - - - ctattgc
- - - - - - - - - - - - - - - - - - - gttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttgc
