Sequence
atgc intronic sequence ATGC exonic sequence...ctggtgaagtgtttcagtttcagttcatttacatgtctagcagagaaaatatctatagactgtgaagaaggaattctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
Basic information
species | Glycine max |
transcript | GLYMA12G30520.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 2
---------------------ctggtgaagtgtttcagtttcagttcatttacatgtctagcagagaaaatatctatagactgtgaagaaggaattc-----taatattg--ccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
|| | | | || || | | | ||| | | | ||| | | |||| | | ||| | || || || ||| |||||||||||||||||||| ||||| | || | ||||||||| |||| || || || ||| |||||||||||| |||||||| || || || || ||||| |
gtgaaaactgcagctttaatcctaattgccacatccttttccaat--aatggtatgcacattggtgtaaaattatgaagacggcacatgtttgtttcctaattggtactgtatcacccatg-ctgcagGTTGGGTACATTGTGACATCTTGCTTATTGAATGAAAATAATGATTTCCTACGGATGGTTATAAATACAGTACGCAATGACATAATAGGACGGAATGAGA
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 2
ctggtgaagtgtttcagtttcagttcatttacatgtctagcagagaaaatatc-tatagactgtgaagaaggaa--ttctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
|| || | | || ||| || | || | || | | ||| || | | | | | || ||| || | | |||||||| |||||||| ||||| | ||||| ||||| || ||||||||| | | ||||||||||||||||||||| || ||||| |||||||| ||||| |
--ggaaccatgcattgtatccaagg-gtttgtatttgcagtttgtattattttatgctcactaccaaatttgcaggtattgaacttttcatccataatttcagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCTATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 2
ctggtgaagtgtttcagtttcagttcatttacatgtctagcagagaaaatatctatagactgtgaagaag----gaattctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
| | || | | || ||| || || | | | | || || | | | || | | | || ||| |||| | |||||||| |||||||| ||||| | ||||| ||||| || ||||||||| | | |||||| |||||||||||||| || ||||| |||||||| ||||| |
-gaaccatgcattgtatctcaag--ggtttgtatttccaatttatattgtttc-atgctccttaactaatttgcaggtattgaacttttcatccatgattacagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCAATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 2
-ctggtgaagtgtttcagtttcagttcatttacatgtctagcagagaaaatatcta-tagactgtgaaga-aggaattctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
| ||| || |||| | |||| ||| || | | || || | | | | | | || | | || | |||| || |||||||| |||||||||||||| ||| |||| || ||||| || ||||||||| | ||||| || |||||||| |||||||||||||| ||||| || |||||||
ttttgtgcag---ttcactgcaagtttattaactttcatcacattacaattggttggttcattacacttttattaactttcatcatattataattggctgcagGTGGGGTACATTGTAACGTCATGTTTACTCAATGAGAACCATGACTTTTTGAGGTTAGCAATAAATACTGTGCGCAATGATATTATTGGCCGAAATGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatatctatagactgtgaagaaggaattctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
ttctaat putative branch site (score: 2)
aattctaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggtgaagtgtttcagtttcagttcatttacatgtctagcagagaaaatatctatagactgtgaagaaggaattctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
- - tgaagtg
- - - - - - - - - - - - - - - acatgtc
- - - - - - - - - - - - - - - - - - - - - -agaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gactgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tattgcc