Sequence
atgc intronic sequence ATGC exonic sequencegcaagcattatgttatactctgagcaatcctttgtcctcttctaccccataagactccttttctctcacattagaatcagaggtgggagcttttttattgagttaaggtttctgttttcagGGGTGACAACAATTGCTGGAGGAAAATGGAGCCGGGGAGGGGGTCATGTTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTTGTTTA
Basic information
species | Glycine max |
transcript | GLYMA01G03880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G03880.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g49770.1 (Oryza sativa), 3'ss of exon 4
gcaagcattatgttatactctgagcaatcctttgtcctcttctaccccataagactccttttctctcacattagaatcagaggtgggagcttttttattgagttaaggtttctgttttcagGGGTGACAACAATTGCTGGAGGAAAATGGAGCCGGGGAGGGGGTCATGTTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTTGTTTA---
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--------cttggtaaaattagaaaggcatgctgccatcatcatgcacatg----------tttgtctaatttgtagtaaacg-ggaaggtcttgacttgga--agtgttctgacatttagGGGTTACAACTATTGCTGGGGGGAAATCAAGCAGAGGAGGG---CATGTTGATGGACCAAGTGATGATGCAAAATTTTCTACTGATTTTGAAGTCCGCTATAT
upper sequence: GLYMA01G03880.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G70280.1 (Arabidopsis thaliana), 3'ss of exon 3
gcaagcattatgttatactctgagcaatcctttgtcctcttctaccccataagactccttttctctcacattagaatcagaggtgggagcttttttattgagttaaggtttctgttttcagGG-GTGACAACAATTGCTGGAGGAAAATGGAGCCGGGGAGGGGGTCATGTTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTTGTTTA
| ||| |||| | || | ||| || | | | || || | ||| | ||||| || | | || | | | || || ||||| ||||| || || ||| | || || || ||||| ||||| ||||||||||| || || ||||| ||||||||||||||||||||
-----------------------gtaatagcttgttcataactgcattcatagaagggttatatat-acgtttgcatcttgtactgag----tttta-------aatgcctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
upper sequence: GLYMA01G03880.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G23880.1 (Arabidopsis thaliana), 3'ss of exon 4
gcaagcattatgttatactctgagcaatcctttgtcctcttctacc-ccataagactccttttctctcacattagaatcagaggtgggagcttttttattgagttaaggtttctgttttcagGGGTGACAACAATTGCTGGAGGAAAATGGAGCCGGGGAGGGGGTCATGTTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTTGTTTA
|| | |||| | || | | | | ||| | | | || | ||| | || | || | | |||| || ||||| |||||||| || ||| | || || || |||||||| ||||||||||||||||| || || ||||| ||||||||||||||||||||
-------------------------------gtgattttttctgcggttttatggttttgccttttggacaaatgtttggtaagtatcggatttaagaaagaataaaaatgc--aatggcagGAGTCACAACCATTGCTGGGGGGAAAATGGTTCGTGGGGGAGGTCATGTGGATGGTCCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
upper sequence: GLYMA01G03880.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0026g00330.t01 (Vitis vinifera), 3'ss of exon 4
gcaagcattatgttatactctgagcaatcctttgtcctcttctaccccataagactccttttctctcacattaga-atcagagg-tgggagcttttttat--tga----gttaaggtttctgttttcagGGGTGACAACAATTGCTGGAGGAAAATGGAGCCGGGGAGGGGGTCATGTTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTTGTTTA
|| | | | || | | ||| | | ||| ||| | |||| || || ||| | || || | | ||| | ||||| | ||||||| ||||||||||| || || || | |||| |||||||| ||||| ||||| ||||||||||| || || |||||||||||||||||||| || ||
-----------------------------gttgtttccagtgtaacagtttagagttgtgatcttctgtgttaaacatcacagaatgagagatcttcaatgctaatattgttgaattttctacctgcagGGGTTACAACAATTGCAGGGGGGAAGCTGGGCCGTGGAGGGGGGCATGTAGATGGGCCAAGTGAAGATGCAAAGTTTTCTAATGATTTTGATGTGGTGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacattagaatcagaggtgggagcttttttattgagttaaggtttctgttttcagGGGTGACAACAATTGCTGGAGGAAAATGGAGCCGGGGAGGGGGTCATGTTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTTGTTTA
ctctcac putative branch site (score: 3)
tttctgttttc putative PPT
ttttttattgagttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagcattatgttatactctgagcaatcctttgtcctcttctaccccataagactccttttctctcacattagaatcagaggtgggagcttttttattgagttaaggtttctgttttcagGGGTGACAACAATTGCTGGAGGAAAATGGAGCCGGGGAGGGGGTCATGTTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTTGTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC