Sequence
atgc intronic sequence ATGC exonic sequence...cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgttttttaatttgagaatcactatgttttttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
Basic information
species | Glycine max |
transcript | GLYMA16G06750.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g03350.1 (Oryza sativa), 3'ss of exon 2
----cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgttttttaatttgagaatcactatgttttttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
| | | | || | | | | || ||| | | || | || | | || ||| | | || ||||| |||||| ||||| | | || || |||||||||||||||||||| || ||||| || ||||| ||||| |||||||| || ||||| || || || || ||
gtcagtcctactatcttcttcatcttcatctgaacgaagaac--------acacgaacga-accaagaaatt---aatctaactgaattcttgaatttttgcagGGGACCTGGCATCGCGGTGCTGATCCTGTCATGGATCATCACGCTCTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGGAAGCGGTTC
upper sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G127338_T02 (Zea mays), 3'ss of exon 1
cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgttttttaatttga-gaatcac---------tatgttttttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
| | | | | || | | | || ||| || |||| || | |||| | | | | |||||| || || | | || || | ||||| ||||||||||| |||||||| || ||||| ||||| |||||||| || ||||| || || || || ||
-------------gtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcagGGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTCCCGGGCAAGCGCTTC
upper sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G40780.2 (Arabidopsis thaliana), 3'ss of exon 2
cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgttttttaatttgagaatcactatgtttt-ttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
| | ||| |||| ||| | || || || | | | | |||| | | | | |||||| |||||||||| || || | | || | | |||||||| |||| || || ||||| ||||||||||||| || |||||||||||||| |||||||| ||||||
-------------gtaaattcccctaaaccaaaaccggtttattttacctaaaccggatttatcaaatcttaacc--ggttttaatttgttttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT
upper sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgtttttta-----atttgaga-atcactatgttttttt-------tcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
| || | ||| | | | || || ||| || ||| | | | || || ||| ||| | || || || | || || || | ||||| || || || | || || || || |||||||| || || || ||||| ||||||||||||| ||||||||||| ||||| || |||||||| |||
-----------ttgaatacatatgta--gttttttaatttcttactacataaatttacttttgatttgattagtaatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
upper sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgtttt---ttaatttgagaatcactatgttttttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
||| | | | | | || ||||| ||| ||| | ||| | || | || | || || | | || | ||| | ||||||||||||||||||| || | | || ||||||||||| || || ||||| ||||||||||||||||||||||| || ||||| ||||| ||| | |||
---gtatgtcttttgtgtctttacaagagatagttgccttattatt-tatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
upper sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S105_62V6.1 (Physcomitrella patens), 3'ss of exon 2
cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatacta---tactatgc----gtttttt-----aatttgagaatcac-tatgttttttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
| || ||| | | ||| || | || ||| | || | || ||| ||||| | | ||||| ||| | | | || || |||||||| ||| | | || || |||||||||||||||||||| | |||||| ||||| ||||| || ||||| ||| || || || | || |||
--gtattaacttcactatatttgaaagcaattcctgtcgcgttctcttatttcctcgcttgctctgccaccgttttctccaacattttgataatgatgtgggcgttcttgtagGGGTCCAGGTATCCTAATGCTCATTCTGTCATGGATCATCACCCTCTTCACTCTCTGGCAGATGGTGGAAATGCACGAAGCTGTCCCGGGTAGGCGGTTT
upper sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_71V6.1 (Physcomitrella patens), 3'ss of exon 3
-cttccatgacctcaaagaaataaaaaaagataaacaactt--tttagtatatatactatactatgcgttttttaatttgagaatcac-tatgtttt---ttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
|| | || || | | | | | | | ||| | | | | | | | | |||||| || || | || | ||| |||||||| ||| | | || ||||| |||||| |||||||||| | ||| || ||||||||||| |||||||| ||| || || ||||| || ||
gtatcaaccactacaccacagccagttcacgtttccttcctattttccttccgccattgttcccttctccacaaactttgaggatgacgtgggtatcatgtttgtagGGGTCCAGGTCTCCTAATGCTCATCCTTTCATGGGTCATCACCCTCTTCACACTCTGGCAAATGGTGGAGATGCACGAAGCTGTGCCCGGAAAGCGATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatatactatactatgcgttttttaatttgagaatcactatgttttttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
ttttaat putative branch site (score: 3)
ctatgttttttttc putative PPT
ttttttaatttgagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgttttttaatttgagaatcactatgttttttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - catgacc
- - - - - - -aaagaaa
- - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - gataaac