Sequence
atgc intronic sequence ATGC exonic sequence...tcaatgatttccatcctttcgaataaattagtggcatacatgtttctataaacatttataaaatcacgcgtcttcactaattcttgttgaatgtgctcagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCATGGTTGCACTGGTGTGGCAGCTAGAGCCTGTGGTCTAGTGGGACTAGAACCCACTAGG
Basic information
species | Glycine max |
transcript | GLYMA08G21610.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G21610.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 4
tcaatgatttccatcctttcgaataaattagtggcatacatgtttctataaacatttataaaatcacgcgtcttcactaattcttgttgaatgtgct----cagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCATGGTTGCACTGGTGTGGCAGCTAGAGCCTGTGGTCTAGTGGGACTAGAACCCACTAGG
|| | | |||| | |||| | | | || || | || ||| | || || ||| || | | ||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||| | |||||||| |||||||| || || || || |||
--------------gtattttattcctctagttttgtttttgttaat-tggatatagttattctgctttttcctcaatggttgtttttgtattttccgtaacagCCTGGTCCGGATTCCATTGGAATCATCGCTATTTCTCATGGTTGCACTGGTGTGGCAGCACGCGCCTGTGGCCTAGTGGGTCTTGAGCCTACAAGG
upper sequence: GLYMA08G21610.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g03740.t01 (Vitis vinifera), 3'ss of exon 4
--tcaatgatttccatcctttcgaataaattagtggcatacatgtttctataaacatttataaaatcacgcgtcttcactaattcttgttgaatgtgctcagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCATGGTTGCACTGGTGTGGCAGCTAGAGCCTGTGGTCTAGTGGGACTAGAACCCACTAGG
|| | | | | | | | || | | || || | | | | | | | ||| || | |||| | ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||| || || ||||| ||||| || || |||
atctaaggggtattcctttataacttttgctgccgaaatttctctctccatga-cttggttgatagtattttcctttgaaaact-ttgtatgacgtgtgcagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCATGGTTGCACTGGAGTGGCAGCACGAGCCTGCGGCCTGGTGGGTCTAGAGCCTACAAGG
upper sequence: GLYMA08G21610.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S15_11V6.1 (Physcomitrella patens), 3'ss of exon 5
tcaatgatttccatcctttcgaataaat--tagtggcatacatgtttctataaacatttataaaatcacgcgtcttcactaattcttgttgaatgtgct-cagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCATGGTTGCACTGGTGTGGCAGCTAGAGCCTGTGGTCTAGTGGGACTAGAACCCACTAGG----
| |||| || | | ||| || || || || || | | | || | | | || || | | | || | ||||||||||||||| ||||||| ||| ||||||| || ||||||||| || | |||||| |||| || || || | || || || | |
---ttaatttaggagctaacaaggtaatgatattgattctttaattcaaattaaagtggttgattgcaaatgccattgctgatacgtcactagtgcaatgcagCCTGGTCCGGATGCCATTGGCATCATTGCTATATCCCATGGTTGCGTGGGCATAGCAGCTCGAGCGTGCGGCCTTGCGGCGCTCGATTTTAGCAAAGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctataaacatttataaaatcacgcgtcttcactaattcttgttgaatgtgctcagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCATGGTTGCACTGGTGTGGCAGCTAGAGCCTGTGGTCTAGTGGGACTAGAACCCACTAGG
cactaat putative branch site (score: 2)
aacatttataaaatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaatgatttccatcctttcgaataaattagtggcatacatgtttctataaacatttataaaatcacgcgtcttcactaattcttgttgaatgtgctcagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCATGGTTGCACTGGTGTGGCAGCTAGAGCCTGTGGTCTAGTGGGACTAGAACCCACTAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - -tccatcc
- - - - - - - - - - - - - - - - -gcataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgttg