Sequence
atgc intronic sequence ATGC exonic sequencegtactttatcttaactgtacctattgaaactgaagactgtaacatgctgattgttcttgcttgaaaattgtcagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
Basic information
species | Glycine max |
transcript | GLYMA04G05910.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------------------------------------gtactttatcttaactgtacctattgaaactgaagactgtaacatgctgattgttct-tgcttgaaa-------attgtcagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
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gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcat-ttggttgttaacagagtgatattattattttcctgtgatagATATCCATGCACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA------------------
upper sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
----------gtactttatctt---aactgtaccta----ttgaaactgaagactgtaaca-tgctgat----tgttcttgct-tgaaaattgt---cagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
||| ||||| || | | || || | | | | | || ||| |||| |||| ||| | | | ||| |||| | | || || ||||| ||||| ||||| ||||| ||||| |||||||| | ||||||||| ||||||||||| || ||| | |||||||| ||
attcaactcagtattttattttgtaagttataactggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatattcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
upper sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G463904_T03 (Zea mays), 3'ss of exon 24
--------------------------gtactttatcttaactgtacctattgaaactgaagactgtaacatgctgattgttcttgcttgaaaattgtcag-
| |||| | | ||||| | || | || | | | || | ||| | | |||| || || | ||| ||||| ||||| || |||||||| ||||| || |||| ||||||||||| ||||||||||| |||||| | || || ||
cctgagttcagaattcaaatatgctgacaacttatgtgacttgtacggctgttaattaaataatattactaatgcactgtgacagataaccttgcttcagCATCAAACAACATTCATCCCAAGCTTGTGATCCTCCACATGAACATGGCCCTCTATGTATATGATGATATAATGAGGATGACTGAAAACTTGAGCGAAAA---
upper sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G463904_T01 (Zea mays), 3'ss of exon 23
-----------------------------------------gtactttatcttaactgtacctattgaaactgaagactgtaacatgctgattgttcttgct---tgaaaattgtcagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
| |||| | | ||||| | || | || | | | || | ||| | | | || || || | ||| ||||| ||||| || |||||||| ||||| || |||| ||||||||||| ||||||||||| ||
ttttcattcttatctcctgagttcagaattcaaatatgctgacaacttatgtgacttgtacggctgttaattaaataatattactaatgcactgtgacagATAACCTTGCTTCAGCATCAAACAACATTCATCCCAAGCTTGTGATCCTCCACATGAACATGGCCCTCTATGTATATGATGATATAATGAGGATGACTGA------------------
upper sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 16
lower sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 24
-----------gtactttatcttaactgtacct-attgaaactgaagactgtaacatgctgattgttcttgcttgaaaattgtcagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
|| | | ||| | | | | | || | | | | | || || || | | ||||| | ||| || | || ||||| || || ||||| ||||| |||||||| || || || || ||||||||||| ||||| || || ||||||||||||||
gtctactctccaaaccactttacgaatgttcttcacctacaatgtaatccaatagttaatccttaaatttcctggtga--catcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA
upper sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 24
-----------------------------gtactttatcttaactgtacctattgaaactgaagactgtaacatgctgattgttcttgcttgaaaattgtcagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
| | | | | | | ||| |||||||| | | || | | | | | ||| || |||||| |||||| | || ||||| ||||| |||||||||||||||||||| |||||||| || ||||||||||| ||||| |||||| | |||||||||||
ttatatctgtatcccttaatatattttgaaaaatgtgttactattttcccttttgaaacttc---tctccatctactaactaatgtagtttgctaaacaacagTTACATACTCAACACCGAAGCTGGTGATCCTTCACATGAATATGGCACTGCATGTGTACGAGGATATCATGAGAATGACGGAAAACTTGAGTGAGAAGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctattgaaactgaagactgtaacatgctgattgttcttgcttgaaaattgtcagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
tgctgat putative branch site (score: 3)
ttgaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttatcttaactgtacctattgaaactgaagactgtaacatgctgattgttcttgcttgaaaattgtcagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT