Sequence
atgc intronic sequence ATGC exonic sequence...atagttgtattattatttatttttttggccaaaaaagtaagaagagagcgttaattaaaatttgttcacattgattatcatttgttgtcactacttgcagGAGGTTATGACAAAGAAGAAAAGGCAGCTAGAGCCTACGATTTGGCAGCACTAAAATACTGGGGAACAACTACGACAACAAATTTTCCA
Basic information
species | Glycine max |
transcript | GLYMA18G47980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g42570.1 (Oryza sativa), 3'ss of exon 4
--------------------------------atagt-tgtattattatttattt-ttttggccaaaaaagtaagaagagagcgttaattaaaatttgttcacattgattatcatttgttgtcactacttgcagGAGGTTATGACAAAGAAGAAAAGGCAGCTAGAGCCTACGATTTGGCAGCACTAAAATACTGGGGAACAACTACGACAACAAATTTTCCA
|| | | || || || ||| ||| | |||||| | || | |||| |||| || | || || || || | || ||| ||||||||||||||||| ||||| ||| | || || ||||||||||| |||||||||||||| || || || ||||||||||| |||
gtaagagctaatcttgtgcaatatattcacctatcatgtatagcat-atatatccatttcgtaaaaaaaaatgtaaatcttatgctaatacttcgaagttctcacttatcttc-ttcacgaacatt-tgtgtagGCGGTTATGACAAAGAAGATAAGGCGGCTCGGGCTTATGATTTGGCAGCTCTAAAATACTGGGGCACGACCACAACAACAAATTTCCCA
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G17430.1 (Arabidopsis thaliana), 3'ss of exon 4
atagttgtattattatttatttttttggccaaaaaagtaagaagagagcgttaattaaaatttgttcacattgattatcatt-tgttgtcactacttgcagGAGGTTATGACAAAGAAGAAAAGGCAGCTAGAGCCTACGATTTGGCAGCACTAAAATACTGGGGAACAACTACGACAACAAATTTTCCA
||| || || ||||| ||| | ||| | || |||| | | | | || | | || || || |||| || | | ||||||||||||||||||||||||| |||||||| || |||||||| || |||||||| || |||||||| || || || || || || ||
------gtaa-gttcttgattttaagctataaattaataatagatgactattaaatctattctaagcaaaat-ataattgttgtgttatctgatcctacagGAGGTTATGACAAAGAAGAAAAAGCAGCTAGGGCTTACGATTTAGCCGCACTAAAGTATTGGGGAACCACCACTACTACTAACTTCCCC
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------------------------------atagttgtattattat----ttatt--tttttggccaaaaaagtaagaagagagcgtta-attaaaatttgttcacattgattatcatttgttgt-cactacttgcagGAGGTTATGACAAAGAAGAAAAGGCAGCTAGAGCCTACGATTTGGCAGCACTAAAATACTGGGGAACAACTACGACAACAAATTTTCCA
| ||| || || | | ||| | | ||| || ||| || | | | ||| |||| | | ||| || || || || |||||| ||||| ||||||||||||||||| ||||||||||| |||||||| || ||||||||||| | | || || | || |||||
gtatgactggagggacttgaagcacagaaccctctccatgtgcttccttctgagccgttgtgaagttcaaagaacagtctgctgaaagtttgagctagaacagtcattggatgatcaggcgatgattgctatgtggtgaaggttgtatacgcagcatctcacgatctaatgtgtttgggc--actgtcacgtgctgcgcagTATACTTAGGAGGATATGATAAAGAAGAAAAGGCAGCCAGAGCCTACGACTTGGCAGCGCTCAAATACTGGGGTCCCAGCACCACCATCAACTTTCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagcgttaattaaaatttgttcacattgattatcatttgttgtcactacttgcagGAGGTTATGACAAAGAAGAAAAGGCAGCTAGAGCCTACGATTTGGCAGCACTAAAATACTGGGGAACAACTACGACAACAAATTTTCCA
cattgat putative branch site (score: 4)
ttaattaaaatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagttgtattattatttatttttttggccaaaaaagtaagaagagagcgttaattaaaatttgttcacattgattatcatttgttgtcactacttgcagGAGGTTATGACAAAGAAGAAAAGGCAGCTAGAGCCTACGATTTGGCAGCACTAAAATACTGGGGAACAACTACGACAACAAATTTTCCA
- - - - - - - - - - - - - - - aaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtc