Sequence
atgc intronic sequence ATGC exonic sequence...gtattttgatatggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtttctaaatttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
Basic information
| species | Glycine max |
| transcript | GLYMA18G46460.1 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46460.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g42820.1 (Oryza sativa), 3'ss of exon 1
gtattttgatatggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtt--tctaaatttggtgctaatggtgcaatgttattttg-gtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
|||| | |||||| | || || | | | | | | | | || || | | | | || ||| || | || |||||| | |||||| || |||||||||||||| || |||||| | |||||||| ||||| ||||| || | || | ||| ||||| || ||
gtatgtatatatggcatcgatcggccctgcaacatgttcagtttttattaggtaattaaatcaactatcacatttttcgttcaaaacatttacgcatctgcagATGTGTAACTACTCTTCGATGGATGGTGTCCTGTACTGCAAGACGCACTTTGAGCAGCTCTTCAAAGAGACGGGGAGCTTCTCAAAGAAATTCTCGCAAG
upper sequence: GLYMA18G46460.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
gtattttgatatggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtttct-------aaatttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
| | | || | | | |||||| | ||| | || | || || || | | ||||| | |||||| || |||||||| || | ||||||||| | || ||||||||||| ||||| |||||||| |||||||||||||| || |||||||
-------------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
upper sequence: GLYMA18G46460.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G45800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtattttgatatggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtttctaaatttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
|||||| | | || | | | | ||| || | | || ||| ||| || ||| | || | || | ||| |||| | || ||||| ||||||||||| || || || || ||||||||||| |||||||||||||| ||||||||||||| ||||||||| ||||| |||
gtatttctcttttcttcttcttcctccattgtta---ctctgtttttcgacaatgcttc---att--gttttaaaagaccacatcttttcttaacac-agATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
upper sequence: GLYMA18G46460.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
gtattttgatatggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtttctaa--atttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
| | | | | | | | | | || | | | | || | | || | | | | ||| | | |||||| || ||| ||||| ||||| || || | || |||||| | || ||||| || || |||||||||||||||||||||||||| ||||||||| |||
-----------------------gtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatggc-agATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
upper sequence: GLYMA18G46460.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g03370.t01 (Vitis vinifera), 3'ss of exon 1
-----------------gtattttgata-tggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtttctaaatttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
|||||| || ||| || | | | | || | | | || || | ||||||| || ||| |||| | ||||||| || |||||| || |||||||| |||||||| ||||| || || ||||| ||||| |||||||| |||||||||||||||||||| |||||||||
gtatgtttcttctaagcctatttttcccctgtttttttttttttttggtaaatttttacgaaaatcaatatc-tacgtaaatttatga--gatataacaagtgggttttactttgcagATGAGCAACTACTCATCCATGGATGGGGTCCTCTACTGCAAACCTCATTTTGAGCAGCTGTTCAAGGAGTCTGGCAATTTCAGCAAGAATTTTCAAACAT
upper sequence: GLYMA18G46460.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S80_3V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtattttgatatggtttgatt--caaggaaagaagaaatatatgtagtt-taaaattgtttctaaatt-tggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG-
| ||||| | || | | | | || | | | | |||| | | | |||| || | || |||||| ||| | | | | | ||| | | ||| | || | || || || ||||| ||||||||||||||||| |||||||| |||| |||| | ||| ||||| |||| ||||
tctcttttgttctgttaagtcttcctagcactaaccgagtcgctgtacctatcagcctgttataaagctacggagctaat----taatatc-tgtgtgcaaacagCTTGCAAACTATGCGTCTCTAGAAGGAGTGCTCTACTGCAAGCCACACTTTGAGCAGCTTTTAAAGGTCACTGGGAGTTTTGACAAGAG-TTTCGAACACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaaattgtttctaaatttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
tgctaat putative branch site (score: 2)
ttatttt putative PPT
aattgtttctaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttgatatggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtttctaaatttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - tgatatg
- - - - - - - - - - - - ggaaagaa
- - - - - - - - - - - - - - - - - - - tatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgca
