Sequence
atgc intronic sequence ATGC exonic sequence...cccttgtaatgatttgatctgggcttctttattttaaaataaaggatatggaatagggaaaccaaaattgtcctcacaagttttcatgcttcctgttcagCAATATGCATGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
Basic information
species | Glycine max |
transcript | GLYMA09G38740.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 5
cccttgtaatgatttgatctgggcttctttattttaaaataaa--ggatatggaatagggaaaccaaaattgt----cctcacaagttttcatgcttcctgttcagCAATATGCATGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
| || | | || ||| |||||| | | | ||| | ||| | ||||| | | | | | | | | | ||| ||||| | ||||||| || |||| | |||||| ||||||| || ||||||||| | |||| ||||| |||| |||||| ||| || ||||||||||| |||||||| |
----tagaaag-taagaattggtactctttaatatcagggaaattcaacatgatagagggagatatataccatacttctttttacatacttatg-ttcctttgcagCAATTTGAATGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCT
upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 5
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 5
cccttgtaatgatttgatctg---ggcttctttattttaaaataaaggatatggaataggga----aaccaaaattgtcctcacaagttttcatgcttcctgttcagCAATATGCATGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
| || || || || | | || || | || || | || ||| | | | || |||| || || | | ||| || ||||||| || |||| | |||||| |||| ||||| ||||||||| || |||| ||||| |||| | |||||| || || || |||||||||||||||||||
-----gaaaagagatggactatataattacattccttgataaataaagtaataaaatgtttactttatctgaatttgttgccatgtgtgtgttttctttttg--cagCAATTTGAATGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTT
upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 5
-cccttgtaatgatttgatctgggcttctttattttaaaataaaggatatggaatagggaaaccaaaattgtcctcacaagttttcatgcttcctgtt-cagCAATATGCATGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
| ||| | | ||| || | | || | | | | || | || |||| | || || | | ||| | || ||||||| || ||| | ||||| |||||||| ||||||||| || |||| ||||| |||| | |||||| || || ||||| ||||||||||||||||
tgctgcaccatgcctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccat--gtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 5
cccttgtaatgatttgatctgggcttctttattttaaaataaaggatatggaatagggaaaccaaaattgtcctcacaagttttcatgcttcctgttc-----agCAATATGCATGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
| | | | || ||| ||||| | | | || | | | || ||| | ||| | || |||| || | || ||||||||| |||||||||||| |||||||||||||||||||||||| ||| || ||||||| ||||| | ||| ||||| |||||||||||||||||||
----tttcacgtttaatagtggaactcttttcatgatgacaatctttgcaaagtttt-aagccagacttgggtttggtgtttgacatgtttattttttcttctagCAATATGAATGGCTTGTTGGTTCACAATACAAACCAATGGAGTTGCTAAAGTCTGACTGGGCAGCAATCAGGAAATCTCCACCATGGGCCATTGATTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatggaatagggaaaccaaaattgtcctcacaagttttcatgcttcctgttcagCAATATGCATGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
tcctcac putative branch site (score: 2)
ttttcatgcttcct putative PPT
aaaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccttgtaatgatttgatctgggcttctttattttaaaataaaggatatggaatagggaaaccaaaattgtcctcacaagttttcatgcttcctgttcagCAATATGCATGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
cccttgt
- - - - -tgatttg
- - - - - - - - - - - gcttctt
- - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgct