Sequence
atgc intronic sequence ATGC exonic sequence...ttatacttaattccacttaggacgaattataaaatatctgaaagcaattgttaaactcttgtggatttgacttcagattttgcatatgaattgttgatagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG
Basic information
species | Glycine max |
transcript | GLYMA09G40480.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
--ttatacttaattccacttaggacgaattataaaatatctgaaagcaattgttaaactcttgtggatttgacttcagattttgcatatgaattg-ttgatagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG
|| | || | | | || || ||| || | || || | | | || || || || |||||| || | ||| ||| | ||||| ||||| ||||| |||||||| |||||||| ||||||||||| |||||||||||||| || |||||| |||||||||| |||
gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgctaattt---gttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 6
ttatacttaattccacttaggacgaattataaaata-tctgaaagcaattgttaaactcttgtggatt----tgacttcagattttgcatatgaattgt-tgatagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG
| | | | || ||| || | ||| | || | ||| || ||| || || || || || |||| | | ||| ||| | ||||| ||||| ||||| |||||||| |||||||| ||||||||||| ||||| |||||||| || |||||| ||||||||||| | |
------gtgctgctagttgcagtcttccatattttagtttgagaatcatgataaaatcttttatcattcttatgttctcttcttatggtggtggattgcctcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACATGTGTTTCTCGTTTTGAAAATCTACATCTTGTTG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 6
-----ttatacttaattccacttaggacgaattataaaatatctgaaagcaattgttaaactcttgtggatttgacttcagattttgcatatgaattgttgatagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG
||| |||| | | | | |||||| | || || |||| | | | | || | |||| | | | ||||||| || || | | || || || || || || || ||||||| |||||||||||||| |||| |||||||| || ||||| ||||| ||||| | |
ttgggttagctgacattcaaacctgattaatcttgaaaataccaatggatgataagaaatgtcttctatgtataaatt--gtttttttctgt---tcactgatagGCAATAGTAAAACTGGCGGAGGAAGAAGGAAACTATCTACAAGATGCTTGGGAGCATATACTGACTTGTGTTTCACGGTTTGAGCATCTTCATCTCTTGG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 6
ttatacttaattccacttaggacgaattataaaatatctga-aagcaattgttaaactct---tgtggatttg-acttcagattttgcatatgaattg--ttg-atagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG
|| || |||| | ||| | || | || | | | || | ||| || ||||| |||| | || ||| | ||| || ||||||||||| ||||| |||||||| |||||||| || || ||||| ||||| ||||| ||||| || || ||||| ||| | ||||| | |
--------tatggtgtgagcgataaattcttgaattttaagcaaatgaccatttgcttttaaatctgaagttgtgattgtgatttggcattctactttgtttgtacagGCAATAGTTACTATTGCAGATGAAGATGGGAACTACTTACAGGAGGCCTGGGAACATATTTTGACATGTGTGTCTCGGTTTGAGCATTTGCATCTCTTGG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S264_74V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------ttatacttaattccac----ttaggacgaattat-aaaatatctgaaagcaattgt-taaactcttg-tggatttgacttca----gattttgcatatgaattgttg----atagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG
|| || || | | | | | | | | | || |||| | || | || | | ||| | | || || | | | | |||| | |||| | ||| ||| || | || || ||||| || ||||| |||||||| || |||||||||||||| |||||||||||||| || || || ||||| |||||| | |
gtattgacgcttttatggtcctggctatgttatttacaaacgttttatttgaatacgcgacctccaaatgtacagttgaaggatctcagttgctttatgtacatttttgctacacgagaatttatgaggttctctaatatccactgttacatcacagGCAATTATTTCAATCGCAGATGAAGACGGGAACTACTTACAGGATGCTTGGGAGCATATTTTGACCTGTGTTTCGCGCTTCGAGCATCTTCATCTTATTG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S11_55V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------ttatacttaattccacttaggacgaattataaaatatctgaaagcaattgttaaactcttgtggatttgacttcagattttgcatatgaattgttgatagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG
| || | |||| | ||| | || | | ||| | || ||| | | | | | | | || ||| || || | ||||| || |||||||| || |||||||| || || |||||||| || ||||| || ||||| || ||||||||||| |||||| | |
gtattaagcgcttttataatcctgaataaattttgttgaaatgtttactttgccgagcaacctccaaatgtacttgtcaggaacctccgctgctttgtatatacttggttg-ttcgcacagatatcaagctcttctaacggtctatttggatggcagGCAATCATTTCCATTGCAGACGAGGATGGAAACTACTTACAGGATGCCTGGGAGCACATTTTGACATGCGTTTCGCGCTTTGAACATCTTCATCTTATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgttaaactcttgtggatttgacttcagattttgcatatgaattgttgatagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG
atttgac putative branch site (score: 4)
atatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatacttaattccacttaggacgaattataaaatatctgaaagcaattgttaaactcttgtggatttgacttcagattttgcatatgaattgttgatagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - ccactta
- - - - - - - - - - - - - - ataaaata
- - - - - - - - - - - - - - - - - - -ctgaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatat