Sequence
atgc intronic sequence ATGC exonic sequencegtgaaattatcacattgttagagacttagagtaaatattgttttcttatatgtattggatacacttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC
Basic information
species | Glycine max |
transcript | GLYMA10G00830.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 3
-----gtgaaattatcacattg--ttagag-----acttagagtaaatatt-gttttcttatatgtattggatacacttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC
|||| | || | || ||| | ||| | || | || ||| ||| | | ||| | || || ||||||| |||||||||||||| |||||||| ||||||||||| || | ||||||||||||| || || ||||| || ||||| || ||| | || |
gtatgcctaaatcctttcaataattttgagtgcatatttacatcaattgtttgttctctgagttctatgtttttcatttcacaaagGTTGAGCATGTCAAAGCTGAAAGAAATCTTCTTGCTGAAGTGGATCACCATTGCATTGTTAAGCTATACTGTTCATTCCAAGACAGTGAATATCTGTACC
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
----gtgaaattatcacattgttagagacttagagtaaatattgttttcttatatgtattggatacacttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC
| || | | | || || | | | ||| | || || || | | ||||||||| |||||||| ||||| ||||||||| ||||||| |||||||| |||||||||||||| ||||| |||||||| || |||||||| ||||| || ||||
gtatttaaattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 4
--------gtgaaattatcacattgttagagacttagagtaaatattgtt--ttcttatatgtattggatacacttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC
| || | | | | | | | | | ||| ||| | || | || ||| |||||||||| || ||||| ||||| ||||||||| ||||||| || |||||||||||||||||||| || || |||||||| ||||||||||| |||||||| ||||
gtatctccttcaagctgcttttgtttgatatatctttgtttattatcgttcatgtttgttgaaatctgat---tctttttcagGTGGAGCATGTGAAAGCAGAGAGAAATTTACTTGCAGAGGTTGACAGCAATTGCATTGTGAAGCTGTATTGTTCTTTTCAAGATGAAGAGTATTTGTATC
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
--gtgaaat-tatcacattgttaga-gacttagagtaaatattgttttcttatatgtattg---gatacacttttt-----tcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC
||| | | | || ||| | ||| || | | ||| || | | ||||| ||| ||| || | ||||||||||||| || |||||||| ||| ||||||| || ||||| |||||||||||||| |||||||||||||| || |||||||| |||| | | ||||
gtatgacttctgttggcctggcagacaatttattgtgtgttatatttatttttct-tattgcccgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------gtgaaattatcaca--ttgttagagacttagagtaaatattgttttctt-----atatgtattggatacac-----ttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC
||| || ||| || |||| || || | | || || | | || || || | || | || ||||| || ||||| ||||| |||||||||||||| ||||||||||||||||| || ||||| || | |||||||| |||||||| ||||| || || ||
ccgttgttttcatgcttgatatgcatacaagttcttagggagtttaccttatccttcttgtacttaaccatgtgctttcaacgcaacgtggtcttggcagGTAGAGCATGTTAAAGCAGAGAGAAATCTACTCGCTGAAGTTGACAGCAACTGTATTGTGAAGTTGTATTGTTCATTTCAAGACGAGGATTACTTGTACT
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------gtga-aattatcacattgttagagacttagagtaaatattgttttc-----ttatatgtattggat---acacttt-------tttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC
||| || || | | || || | | || | | ||| | | | ||| |||| || | | ||| || ||||| || ||||| ||||| ||||||||| | ||||| || || || |||||||| ||||| || | ||||| || |||||||||||||||||||| |||
tcatcataagaatgataacaataataatgataaatatttttatcgactatgatagtgaaaaatcatagccattgaattgaaaattttgcggtaattgcagGTGGAGCATGTAAAAGCAGAGAGAAATTTGCTTGCAGAGGTCGATAGCAATTGTATTGTGAAGTTGTATTGCTCGTTTCAAGATGAGGAGTATTTGTATT
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
gtgaaattatcacattgttagagacttagagtaaatattgttttcttatatgtattggatacacttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC--------------
|| ||||| ||| || | | | | ||| | | | ||||||||||| || ||||| | ||| ||| | ||||| || || || |||||||| ||||| || || ||||| | ||||||||||||||| || || ||||| ||||
-------------gttattagactcttgc--caatcactccggtgctg-atgctctcgtga---ttttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagagacttagagtaaatattgttttcttatatgtattggatacacttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC
cacttttttc CT-rich tract
agtaaatattgttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaattatcacattgttagagacttagagtaaatattgttttcttatatgtattggatacacttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG