Sequence
atgc intronic sequence ATGC exonic sequence...cccccccacccccatcatatggatacccatattaatccagttttttttgtcttcatcatatatttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
Basic information
species | Glycine max |
transcript | GLYMA04G36770.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g40740.1 (Oryza sativa), 3'ss of exon 6
-------cccccccacccccatcatatggatacccatattaatccagttttttttgtcttcat-catatat-ttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
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gttagtggttttacattaaaatca-gtcatcaactattctgctccc-ctcttttcaccttaatatttctgtattatgagcagtagtaaattgtgttctttttcctacagGTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAG
upper sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 3
------cccccccacccccatcatatggatacccatattaatccagttttttttgtcttcatcatatatttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
| | | || | || | ||||||| | | | | ||| | || | || |||| | ||||| || || || ||||| | |||||||| |||||| |||| ||||||||||| |||||||||||||| ||||||||
aggacagacatatattcatttctttcccatgctcatattatact--tctatattgccatctagccagtttaagacattct--ttatttatctttttt--tttgcagGTTCTTTACAAGCATAAGATTGTTCTATTTGGTGGCTTTTATGACACTCTTAGGGAAGTGAG
upper sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 6
cccccccacccccatcatatggatacccatattaatccagttttttttgtcttcatcatat-atttgtttgttctaatgctttattttggttaa--ttaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
| | | | || || | ||| | || | | | | || | || || | | |||| | | | | | || |||||||| |||||||||||||| || ||||||||||||||||||| ||||| | ||||| ||
---gtggagttgtactactttcattatcaatctgttcctgccttcccttttgtaaccaactcatcaagttctcatcctgctctgctataatctactttttcagGTATTATACAAGCACAAGATCATAATTTTTGGTGGCTTCTATGATACTCTACGTGAAGTAAG
upper sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 6
cccccccacccccatcatatggataccca--tattaatccagttttttttgtcttcatcatatatttgtttgttctaatg-ctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
| | | ||| || ||| || || || ||| | || || | || || || | | |||||||||| | | |||||| || |||||||||||||||||| ||||||||||||||||||||||||| |||||||| ||
---ctgtattctataggaatgtatcataggtcatttattcatcttatttgatattttgcactttttcactttttaaattaattttattttggacatgttacagGTTTTATACAAGCACAAGATTATTGTTTTTGGTGGCTTCTATGACACTCTCAGAGAAGTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtcttcatcatatatttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
tttattttggttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccccccacccccatcatatggatacccatattaatccagttttttttgtcttcatcatatatttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
ccccccc
- - - - -ccccatc
- - - - - - - - - - - - acccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaatgc