Sequence
atgc intronic sequence ATGC exonic sequence...gttttcttatttcaaatttgttggttatgattttggcttagaattttctgttgggtcctgacccatgacgcatgcacattacaattttgttatcttgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCGGTGA
Basic information
species | Glycine max |
transcript | GLYMA20G02500.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 3
gttttcttatttcaaatttgttggtt-atgattttggcttagaattttctgttgggtcctgacccatgacgcatgcacattacaattttgttatcttgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCGGTGA
| || | | || |||| || || || | | | | | | || | | | ||| | | || | ||||||| |||||||| |||||||| || ||||| ||||||||||| || || || | || || || | || || | || || || || || || ||
ctggtcatttaacacatttaccattttattgattattccaaatgatgtatataccagtctaattcccaa-acatatatgccgccccattatggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTGACATTTCCACCGTCACGACTGTAGTTAGGGGAGTCGGTGACATTGGGGA
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G033724_T02 (Zea mays), 3'ss of exon 4
gttttcttatttcaaatttgttggttatgattttggctt--agaattttctgttgggtcctgacccatgacgcatgcacattacaattttgttatcttgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCGGTGA
| | ||| ||||| || | || | | | | | || || || | | | ||| | || | | | | |||||| |||||||| || |||||||||||||||||||||||||| | || || | || || || | || || || | ||||| || || || || ||
-gctgatgattccaaatgatttacacaatgttctaattcccaaacatacatgccatgttctaattcccaa-acatacgtgctatgttctaatgaatctgcagAGACATTTGTACGTGCTGATGGGGCATTCATCCCATTTGCTCATGACTTTGACATCTCCACAGTCACAACTACAGTTAGGGGTGTTGGTGATATTGGGGA
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G102346_T01 (Zea mays), 3'ss of exon 4
--gttttcttatttcaaatttgttggttatgattttggcttagaattttctgttgggtcctgacccatgacgcatgcacattacaattttgttatcttgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCGGTGA
| || | || | || || | ||| | | | || | |||| | | ||| | || | | | | | |||||| |||||||| || || || |||||||||||||||||||| | || ||| | || || || | || || || | ||||| || || || || ||
atgattccaaatgatgtacacaatg-ttctaattcccaaacatacatgcatgccatggtctgattcccaa-acatacttgctatgttgtaatgagcctgcagAGACATTTGTACGCGCCGACGGGGCATTCATCCCATTTGCTCACGACTTCGACATCTCCACAGTCACAACTACAGTTAGGGGTGTTGGTGACATTGGGGA
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G45030.1 (Arabidopsis thaliana), 3'ss of exon 4
gttttcttatttcaaatttgttggttatgattttggcttagaatt--ttctgttgggtcctgacccatgacgcatgcacattacaattttgttatct-tgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCGGTGA
|| | || | | |||| || |||| || | || | | ||| | | | | ||| | | | ||||||||||||||| ||||||||||| || ||||| |||||||| || || ||||||| ||||||||||| ||||||||| ||||| | || ||||| |||||
-------------------gtagcctagtaacaatgtatagagttaactctgatgtataatggcgtagcacgattttaattatcggtttctctctttctgcagAAACATTTGTTCGAGCTGATGGAGCCTTCATTCCATTTGCCGAGGACTTCAATACGAACAATGTAACCACAACTGTCAAAGGGATTGGTGAGATTGGTGA
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G35155.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------gttttctta------tttcaaatttgttggttatgattttggc----ttagaattttctgttgggtcctgacccatgac-gcat---gcacattacaattttgttatcttgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCGGTGA
|||| || | || | | ||| | |||| || || | |||| | |||| |||| | ||| || || | | | ||||||||| |||||| |||| ||||| || || || || ||||||||||||||||| | || |||||||| || |||| || | || ||||| || ||
gtactccagttataatttcatagcaaatctctgcatctttctgttcaggaactggcatatttggacactcttgtttcatactgagtactgactatacagggcatctttcatatctatcccaatgcagAAACGTTTGTGAGAGCGGATGGTGCCTTTATTCCTTTTGCAGAAGATTTCAACACGAGCAATGTAACTACGTTGATAAAGGGCATTGGTGAGATAGGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgttgggtcctgacccatgacgcatgcacattacaattttgttatcttgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCGGTGA
tcctgac putative branch site (score: 2)
ttttgtt putative PPT
attacaattttgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttcttatttcaaatttgttggttatgattttggcttagaattttctgttgggtcctgacccatgacgcatgcacattacaattttgttatcttgcagAAACATTTGTGCGAGCTGATGGGGCATTCATCCCATTTGCAGAAGATTTCAATATGAACAATGTAATCACAACTGTAAAAGGTGTAGGGGAGATCGGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - -gttggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcac