Sequence
atgc intronic sequence ATGC exonic sequence...gatatgggttccaattgagtataattccctcatttacaatattatgatgaaaagagcttcatgacattcttattctcattctgcatcacatcttgttcagAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
Basic information
species | Glycine max |
transcript | GLYMA09G41510.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 4
gatatgggttccaattgagtataattccctcatttacaatattatgatgaaaagagcttcatgacattcttattctcattctgcatcacatcttgttcagAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
| ||| ||| | || || | | | | ||| | || | || | | || | || | | | | | || |||||||| |||||||||||||| | ||||| | ||| |||||||| |||||||| || || || || ||||||||||| ||||| || ||||| ||||| |
-gtgaatgttgcaaaggcactgcataagctgctgcattgtttatccatgtgt-gtttttgacgaagtgccctttttt-ttttactt----tttggtgcagAGTTACACACAGTATATTCCGCTTCCTATTACTGATCTTGATTCATGGCTGAAAACACCCTCTATATATGTTTTTGACTGCTCAGCAGCTGGAATGATCG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 3
gatatgggttccaattgagtata-attccctcatttacaatattatg-atgaaaagagcttcatgacattcttattctcattctgcatcacatcttgttcagAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
|| ||| | | | | | | | | | ||| | || | || |||| | | | || | | || | |||| |||||||| ||||| |||||||| | || || | ||| |||||||| |||||||| || || || || ||||||||||| ||||| || ||||| |||||||
-------gtgaatgttgcaaagacactgcataagctgctgcattgtttatccatgtgtgtttttgacgaa---gtgcccttttt---ttactttttgtgcagAGTTACACACAATATATTCCGCTTCCCATTACTGATCTTGATTCATGGCTGAAAACACCTTCTATATATGTTTTTGACTGCTCAGCAGCTGGAATGATTG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 4
--gatatgggttccaattgagtataattccctcatttaca-atatta-tgatgaaaagag-cttcatgacattcttattctcattctgcatcacatcttgtt-cagAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
| || || | | || || | | ||| || ||| | || | | | | || | ||| || || || | | ||| || || |||||||| |||||||||||||| | || || | ||| |||||||| ||||||||||| || |||||||| |||||||||||||| ||| |||| || ||||
gtaaaattatgatgaagacactgta-ttgcttgctttgcatgccttacttatcataggtgtctctgataaattaaaatggtcgttttt--ttgcattttcttgcagAGTTACACACAGTATATTCCACTTCCAATTACTGATCTTGATTCATGGCTGAAGACACCTTCAATTTACGTTTTTGATTGCTCAGCGTCTGGAATTATTG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 4
gatatgggttccaattgagtataattccctcatttacaatattatgatgaaaagagcttcatgacattcttattctcattctgcatcacatcttgttcagAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
| || || | | | || | || ||| | | || | | | | || || ||| |||| ||| ||||||||||||||||| |||||||| || |||| |||||||||||||||| ||||||| || || || |||||||| || |||||||| ||| ||||||||
-gtctgttttttactagcgttttcttttctctaccatgttcttgttccttctcgtctgttaccacgagctgattgattctctgt--------ttgagcagAGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTGAAGACACCCTCCATCTATGTTTTCGACTGCTCTGCTGCTAGGATGATTC
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 4
gatatgggttccaattgagtataattccctcatttacaatattatgatgaaaagagcttcatgacattcttattctcattctgcatcacatcttgttca-gAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
| || | | | | ||| | | |||| | ||| | ||| | | || || |||||| | | ||| | | ||| ||||| |||||||| ||||| || |||| || || ||||||||| ||||||| || ||||| |||||||||||||||||||| |||||||||||||
-----gtattttattactttgaagttctgccgt----gctattttattgatatcgcctttaga----tttttctcctattctgactggtgtattggtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgaaaagagcttcatgacattcttattctcattctgcatcacatcttgttcagAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
tcttgttc CT-rich tract
attcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatatgggttccaattgagtataattccctcatttacaatattatgatgaaaagagcttcatgacattcttattctcattctgcatcacatcttgttcagAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
- - - - - - - - - - - - ttccctc
- - - - - - - - - - - - - - - - - - - - - - - - gaaaagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgac