Sequence
atgc intronic sequence ATGC exonic sequencegttaactaacttaatcaaattttagcaattgtttgttttgttgttagactctaatgattgcaatgtgatgtgatgtggcagATGTGAAAGTGGGGGATGAACTTTTGGTGGATGGAGGAATGGTTAGGTTTGAGGTGATTCAGAAAATAGGTCCAGATGTAAAGTGCCGTTGTACTGATCC
Basic information
species | Glycine max |
transcript | GLYMA20G35400.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g08340.2 (Oryza sativa), 3'ss of exon 3
gttaactaacttaatcaaattttagcaattgtttgt-tttgttgttagactctaatgattgcaatgtgatgtg-----atgtggcagATGTGAAAGTGGGGGATGAACTTTTGGTGGATGGAGGAATGGTTAGGTTTGAGGTGATTCAGAAAATAGGTCCAGATGTAAAGTGCCGTTGTACTGATCC
|||| | | || || || | | ||| | | ||| | || | || | || |||||| | | | ||||||||| ||| || ||||| ||| | || ||||| || |||| | ||||||||||| || ||||| |||| |||||||| ||||||||||| || |||||
gttattt---tcaagcagatctcttctgttggtcttatttatatttctattcccct--ctgtaatgtgttttttgaacactacacagATGTGAGAGTTGGTGATGAGCTTCTTGTTGATGGTGGCATGGCTCGGTTTGAGGTGGTTGAGAAATTAGGACCAGATGTCAAGTGCCGTTGCACAGATCC
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G066290_T01 (Zea mays), 3'ss of exon 2
gttaactaacttaatcaaattttagcaattgtttgttttgttgttagactctaatgattgcaatgtgatgtgatgtggca--gATGTGAAAGTGGGGGATGAACTTTTGGTGGATGGAGGAATGGTTAGGTTTGAGGTGATTCAGAAAATAGGTCCAGATGTAAAGTGCCGTTGTACTGATCC
|| | | || | ||||||||| ||| | || || | | | || || || ||||||| ||| || ||||| || | |||||||| ||||||| | |||||||||||||| |||| ||||| |||||||| ||||||||||| || |||||
-------gtattggcctatttgttaatattgtttgta--gttactgttctttagcg-taacgttgcatctaaatcctacacagATGTGAGAGTTGGTGATGAGCTCCTTGTGGATGGTGGAATGGCTCGGTTTGAGGTGATTGAGAAGATAGGACCAGATGTTAAGTGCCGTTGCACAGATCC
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G078200_T01 (Zea mays), 3'ss of exon 3
-----------------------------------gttaactaacttaatcaaattt-tagcaat-tgtttgttttgtt-gttagactctaatgattgcaatgtgat-----gtgatgtgg-------------cagATGTGAAAGTGGGGGATGAACTTTTGGTGGATGGAGGAATGGTTAGGTTTGAGGTGATTCAGAAAATAGGTCCAGATGTAAAGTGCCGTTGTACTGATCC
| | | ||||| | || | || ||| || || | || || ||| |||| | | || |||| || || | ||||||| |||| || |||||||| || | ||| || ||||||| ||||||||||||||| | || |||| |||||||| |||||||| || ||||||||
gttatccatcaatactgatcttctctcttgagcctacttattgttttaatgatatatgtatcaaaatgactgatgcattagtgttactgtaattttcccgatttgataatgtgtaatataaaaaaaactctacccagATGTCAAAGCTGGTGATGAACTATTTGCGGACGGTGGAATGGCCAGGTTTGAGGTGATTGAAAAGTTAGGGCCAGATGTGAAGTGCCGCTGCACTGATCC
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G22960.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------gttaactaacttaatcaaattttagcaattgtttgtt--ttgt-tgttagactctaatgattgcaatgtgatgtgatgtggcagATGTGAAAGTGGGGGATGAACTTTTGGTGGATGGAGGAATGGTTAGGTTTGAGGTGATTCAGAAAATAGGTCCAGATGTAAAGTGCCGTTGTACTGATCC
| | | | | ||| | ||| | || | || | | | | ||| ||| | |||| || | |||||| | ||| ||||||||||||||||| ||||| || ||||| || ||||| |||||| |||| || ||||| ||||| ||||| | ||||| |||||
gtatatgcaattatgtttatgtaaaagtggaagtgaaaacattagatgaatattatggtgactgcgtatgaaataggaatcatttggtctttgtgtg-tggtgtagATGTAAGAGTTGGGGATGAACTTTTGGTTGATGGTGGGATGGTGAGATTTGAAGTGATTGAGAAGATTGGTCCTGATGTTAAGTGTCTATGTACCGATCC
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g04480.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------gttaactaacttaatcaaattttagcaattgtt------tgttttgttgttagactctaatgattgcaa----------tgtgatgtgatgtggc--agATGTGAAAGTGGGGGATGAACTTTTGGTGGATGGAGGAATGGTTAGGTTTGAGGTGATTCAGAAAATAGGTCCAGATGTAAAGTGCCGTTGTACTGATCC
|| ||||| | ||| | | ||||| || || | || | ||||| | | || | | | || || | |||||||||||| || |||||||| | |||||||| |||||||| |||||||| |||||| |||| || ||||||||||| ||||| || |||||||||||
gtcattatcttagtatcatcttttggttgaaatgtgctacattctttactaaaactaatgaatgcttgtgtttgttgtaacatgcttagatgcacatgtttaatgttcattaaattctcaattgagctttaatctgactcagATGTGAAAGTTGGTGATGAACTCCTTGTGGATGGTGGAATGGTGAGGTTTGATGTGATTGAGAAGATTGGTCCAGATGTCAAGTGTCGATGTACTGATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgtttgttttgttgttagactctaatgattgcaatgtgatgtgatgtggcagATGTGAAAGTGGGGGATGAACTTTTGGTGGATGGAGGAATGGTTAGGTTTGAGGTGATTCAGAAAATAGGTCCAGATGTAAAGTGCCGTTGTACTGATCC
ctctaat putative branch site (score: 3)
tttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaactaacttaatcaaattttagcaattgtttgttttgttgttagactctaatgattgcaatgtgatgtgatgtggcagATGTGAAAGTGGGGGATGAACTTTTGGTGGATGGAGGAATGGTTAGGTTTGAGGTGATTCAGAAAATAGGTCCAGATGTAAAGTGCCGTTGTACTGATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG