Sequence
atgc intronic sequence ATGC exonic sequence...tttttaagttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatgactgaacgtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
Basic information
| species | Glycine max |
| transcript | GLYMA01G34560.1 |
| intron # | 7 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
-tttttaa-gttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatgactgaacgtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
| ||| | | | | | |||| | || | || | ||||| ||| || | ||| || | | ||| | | || || ||||||| | | ||||| ||||| |||||||||||||| |||||||| ||||| ||||| ||||| |||||||| || ||||| |||||||||| | |
gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgcta--atttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 6
---tttttaagttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatgactgaacgtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
| || | | | |||| || || ||| || | |||| | | || | | | | || | || | || ||||||| | | ||||| ||||| |||||||||||||| |||||||| ||||| ||||| ||||| |||||||| || ||||| ||||||||||| |||
gtgctgctagttgcagtcttccatatt-ttagtttgagaatcatgataaaatcttttatcattcttatgttctcttcttatg-gtggtggattgcctcac-agGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACATGTGTTTCTCGTTTTGAAAATCTACATCTTGTTG
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 6
tttttaagttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatga--ctgaacgtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
| | | |||| | | | || | ||||| || ||| |||| | | ||| | || | || | || ||| | | | |||| || | |||||||||| || || || || || ||||| || ||||| ||||| | |||||||||||||| |||||||| |||||||| | |
-tgtcactttttatctcgatgttatttccttcctgatctaactgtcgccttttcccctctaaaattgtctggatcccaaattaatattggttgt-tctccagGCGATTCTCAGACTTGCTGATGAAGAGGGCAACTATTTGCAAGATGCCTGGGAGCATATACTAACTTGTGTTTCCCGTTTTGAGCAACTACATCTCTTGG
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 6
tttttaagttttgggtagtgtattcttggt--acctgaactttgtgttcagtttttgttgattacattatatgactgaac-gtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
|| ||| | | | | || | | || | | | | | | | || |||| | || || | | || | | ||||||||||| | || || || || ||||| || ||||||| |||||||| ||||| ||||||||||||| |||||||||||||| ||||| | |
---ttgggttagctgacattcaaacctgattaatcttgaaaataccaatggatgataagaaatgtcttctatgtataaattgtttttttctgttcactgatagGCAATAGTAAAACTGGCGGAGGAAGAAGGAAACTATCTACAAGATGCTTGGGAGCATATACTGACTTGTGTTTCACGGTTTGAGCATCTTCATCTCTTGG
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 6
tttttaagttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattat-atgactg-aacgtgtcat-ctgttttattacta--gGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
|| | | || | | ||||||| | | || || || || | || | | | ||| || | || ||| || ||| || || |||||||||| |||||| ||||| ||||| || |||||||| || || ||||||||||| ||||| ||||| || |||||||||||| | ||||| | |
----tatggtgtgagcgataaattcttga-attttaagcaaatgaccatttgcttttaaatctgaagttgtgattgtgatttggcattctactttgtttgtacagGCAATAGTTACTATTGCAGATGAAGATGGGAACTACTTACAGGAGGCCTGGGAACATATTTTGACATGTGTGTCTCGGTTTGAGCATTTGCATCTCTTGG
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ24773 (Selaginella moellendorffii), 3'ss of exon 6
tttttaagttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatgactgaacgtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
| ||||| || | || | ||| | ||| || | | | |||| | | ||||||||||| |||||||| || |||| ||||| |||||||| || |||| |||||||| || ||||||||||| |||||| |||
---------------------------------------------gtattttttctttctcctcttttcatactcataatgtaattc--catgctgc-agGCGGTGATATCCATTGCTGATGAAGATGGAAACTATCTACAGGAAGCCTGGGAACACGTCCTGACGTGTGTTTCTCGCTTTGAGCATCTCCATCTTATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagtttttgttgattacattatatgactgaacgtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
tgttgat putative branch site (score: 4)
tctgtttt putative PPT
ttgattacattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttaagttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatgactgaacgtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
- - - - - - -ggtagtg
- - - - - - - - - - - - - - - acctgaa
- - - - - - - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctgt
