Sequence
atgc intronic sequence ATGC exonic sequence...acaaatgtttgggcagagcatcaagcatatgattatgttgcatcattgattgatgtttatatgctgctacctattgtctgacacgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
Basic information
species | Glycine max |
transcript | GLYMA03G02610.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
------acaaatgtt----tgggcagagcatcaagcatatgattatgttgcatcattgattgatgttta-tatgctgctacctattgtctgacacgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
||| || | |||| | | || | || | || ||||| || | || ||| | | || || || | | |||||||| |||||||| |||||||||||||| ||||||||||| |||||||| | |||||||| ||||| || |||||||| | | || || ||||||
gtaagtacagggcttcctatattcagattgcaatgtatttccccatacttt-tctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 7
---acaaatgtttgggcagagcatca--agcatatgattatgt-------tgcatcattgattgatgtttatatgctgctacctattgtctgacacgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
| ||| | || | |||| | | || |||| | ||| || | | | ||||| | | | | | | | | || | | ||||| || ||||||||||||||||| ||||| |||||||| || |||||||| | |||||||| ||||| || |||||||| | | ||| ||||||||
gtaaggaatctgaggctttattatcattactacattgcaatgtgtttttttacatttctgttcggt-cttatagacag-tgcatgattttttttttttttgccctcttgtagGCATTACAATATGAACCGCATCAGACTTGTTTGGTCAAGTATATGGCATGTCTTGTCTGATTTTTTTGTCACCATTGGCTGCTCAGAAAATCTTTCAATC
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------acaaatgtttgggcagagcatcaagcatatgat-tatgttgcatcattgattgatgtttatatgctg-ctacctattgtctgacacgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
|||| || | | ||| || | | | || | | |||| | || | ||| |||| | ||| ||| ||||||| ||||| ||||| ||||| |||||||| ||||||||||||||||| || || || | ||||||||| || ||||| || | | || ||||| |||
gtaagaatctcctagtttcgttcctctctgttctctcata-tactgcatataagagacgttctctgttcttagcaactttaagtatgtagtctgacaattttctgtt--tgtcatt-tgtgacagGCATTATAACATGAATCGCATAAGGCTTGTTTGGTCAAGCATCTGGCAAGTGCTATCAGGTTTCTTTGTGACCATTGGATGCTCAGAGAATCTTTCTATT
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
acaaatgtttgggcagagcatcaagcatatgattatgttgcatcattgattgatgtttatatgctgctacctattgtctgacacgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
| | | ||||| | | | ||| | | | || || || | | || || ||| ||| || | ||| |||||||||||| ||||||||||| || ||||| ||||| |||||||||||||| ||||||||||||||||| ||||||||||||| | ||||| || |||
------------gtaagg-atcaatcttttctttacgatatctgttttgtttttgctcactctctcttatttataccctgtt--tgttgtaatg--gcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 7
-------------acaaatgtttgggcagagcatcaagcatatgattatgttgcatcattgattg---atgtttatatgctgctacctattgtctgacacgattattatgtaa----------------cagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
||| | | | | | |||||| || | ||| ||||| ||| || ||| | ||||||| | | | | | | || || | |||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||||| |||||||||| | ||||||||||||
gtatgaatcattctcaatttgtcttgttcatgttttagcataccatattagtgcttcatttattatttatatttgtcagctgctattaaaaattttgctaaaattctaagtgatttgttttcttttacacagGCACTATAACATGAACCGTATCAGGCTTGTGTGGTCAAGCATCTGGCATGTACTCTCAGATTTCTTTGTAACCATTGGCTGTTCAGAGAACCTTTCAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattgatgtttatatgctgctacctattgtctgacacgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
gtctgac putative branch site (score: 3)
attattatgtaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaaatgtttgggcagagcatcaagcatatgattatgttgcatcattgattgatgtttatatgctgctacctattgtctgacacgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - gtttggg
- - - - - - - - - - -caagcat
- - - - - - - - - - - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacac