Sequence
atgc intronic sequence ATGC exonic sequencegtaagttggtcatggcattatttatgtgtccatgattcattttatttcctgataataatgccttgtacaatatttctaatattgtaacactacagAGGGCATTCTTGGCGACACACTCAGCAAGTTCAGCATATGGGGGCTTTACATAACCTTTGTTCTAGCTGTTGGACGTTTTATCAGACTCCAATGCGCTGA
Basic information
species | Glycine max |
transcript | GLYMA02G16920.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G16920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G065388_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------------gtaagttggtcatggca-ttatttatgtgtccatgattcattttatttcctgataata----atgccttgtacaatatttctaatat------tgtaacactacagAGGGCATTCTTGGCGACACACTCAGCAAGTTCAGCATATGGGGGCTTTACATAACCTTTGTTCTAGCTGTTGGACGTTTTATCAGACTCCAATGCGCTGA
| || | || | ||||| | | | | | | ||| | | | |||| || | || |||| | | | ||||||||||| ||||||| |||||||| || || ||||||||| | | || || || |||||||||||||||| | ||||| || || || ||| | ||
gtatgtatctatccttgccctgagttccctgccaactgtagcatgatctttaaaatctgatagaaattaattttacattctatgaagatgctgattgtttaacaaccacaataatttagtaatgtttagcttgtactcatctctggtgttgtctcaaattttgtctaacaatttatatatctctttttcttctgtccagAGGGCATTATTGGCGAAACACTCAGTAAATTTAGCATATGGAGTTTATATATTACTTTTGTTCTAGCTGTTGCGAGATTTATTAGGCTTCAGTGCTCAGA
upper sequence: GLYMA02G16920.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G48060.1 (Arabidopsis thaliana), 3'ss of exon 19
gtaagttggtcatggcattatttatgtgtccatgattca--ttttatttcctgataataatgccttgtacaatatttctaatattgtaacactacagAGGGCATTCTTGGCGACACACTCAGCAAGTTCAGCATATGGGGGCTTTACATAACCTTTGTTCTAGCTGTTGGACGTTTTATCAGACTCCAATGCGCTGA
| | ||| | | | | ||||| | ||||||| | | | ||| | | || | || || || | |||||||| |||| || ||||| |||||||||||||| |||||||| || || || || ||||| ||||| || || ||||| ||||| || |||||| ||||
----------------gtaagttagctcttc-taattcaagtgttatttcataac--tcatgttctattattgataccgaaaataata----tgcagAGGGCTTTCTGGGTGACACCCTCAGCAAGTTCAGTATATGGGGACTCTATATCACATTTGTACTAGCGGTGGGGCGTTTCATCAGGCTTCAATGCTCTGA
upper sequence: GLYMA02G16920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0104g00760.t01 (Vitis vinifera), 3'ss of exon 19
gtaagttggtcatggcattatttatgtgtccatgattcattttatttcctgataataatgccttgtacaatatttctaatattgtaacactacagAGGGCATTCTTGGCGACACACTCAGCAAGTTCAGCATATGGGGGCTTTACATAACCTTTGTTCTAGCTGTTGGACGTTTTATCAGACTCCAATGCGCTGA
||||||| | ||| | || ||| | | | || |||| | | | || |||| |||| | || ||||||||| |||||||| ||||| || |||||||||||||| ||||| || ||||| |||||||| || || ||||| |||||||||||||| || ||| ||||
gtaagtttaaaa-aacatcgctactgca-----gatgtcgataaaatgttg-taattttccttgttattgtattattaatcctccaattttacagAGGGTATTCTTGGTGACACTCTTAGCAAGTTCAGCATCTGGGGTCTCTACATTACCTTTGTGCTTGCAGTTGGCCGTTTTATCAGACTGCAGTGCTCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttcctgataataatgccttgtacaatatttctaatattgtaacactacagAGGGCATTCTTGGCGACACACTCAGCAAGTTCAGCATATGGGGGCTTTACATAACCTTTGTTCTAGCTGTTGGACGTTTTATCAGACTCCAATGCGCTGA
ttgtaac putative branch site (score: 2)
tacaatatttctaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttggtcatggcattatttatgtgtccatgattcattttatttcctgataataatgccttgtacaatatttctaatattgtaacactacagAGGGCATTCTTGGCGACACACTCAGCAAGTTCAGCATATGGGGGCTTTACATAACCTTTGTTCTAGCTGTTGGACGTTTTATCAGACTCCAATGCGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT