Sequence
atgc intronic sequence ATGC exonic sequence...attgtaaaatggattttttttcgtattttttttatgtggagaagtttgttggatgtagtacatttatggttttgatgtttcttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC
Basic information
species | Glycine max |
transcript | GLYMA17G32980.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1
attgtaaaatggattttttttc--gta-ttttttttatgtggagaagtttgt-tggatgtagtacatttatggttttgatgtttct-tatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC
|| || ||| || ||| | || ||| |||| | | | | | | | ||| | || || | | || | |||||| | || ||||| ||| | || ||||| ||||| |||||| | || || ||||| || || |||||||||||||||||||||||||| ||||| | || |
-----aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaaaatgtttttttttcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
upper sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g19650.1 (Oryza sativa), 3'ss of exon 1
--attgtaaaatggattttttttcgtattttttttatgtggagaagtttgttggatgtagtacatttatggttttgatgtttcttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC
|| || | | || || | | || || | | | | || || | | || ||| | | | | | | ||| | | || ||||||| || ||| | | ||||| || ||||| || | || ||||||||||| || ||||| ||||||||||||||||| || ||||| | || |
gttttatatatatagtgattctttcaacatacttgatcactacatttgttttagagtttatcacttcatgttagtaac--ctgtagttgtttcttttcttagACGCACTACGTCTTGCTATTATGTTCGTTTAAAGAGCAGCTACAGCAGCATGTCCGTGTTCATGCTATGGAAGCAGTAATGGCATGCTGGGAACTTGAAC
upper sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
attgtaaaatggattttttttcgtattttttttatgtggagaagtttgttggatgtagtacattt----atggttttgatgtttcttatggttggatgtt---gcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC
| ||| || |||| || | || | | || | | | | | || |||||| | | | | || | | | || ||| | || ||||| ||| | |||||||| ||||| |||||| | || |||||||| || || ||||||||||||||||| ||||||||||||||| | || |
-----ataattaatcatttt--gtggcaagagcaggttgttatcattctctgttttttccctctttcgaatggttctaaattctaacctgtctcgtttttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
upper sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 2
attgtaaaatggattttttttcgtatttt---ttttatgtggagaagttt-gttggatgtagtacatttatggttttgatgtttcttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC
| | | | || | | | || || | || | ||| | | | | | | || | || | | || || | |||||| |||||||||| ||| | || || || ||||| ||||| |||| |||||||| || || ||||||||||||||||| |||| ||| |||||| | || |
-tctttgtctagggttctgtacatagttaacatcttgcatcatctgtttttgccaggccttcttgttcccagattctaatatattcc-tgtttt--tattgcagACGCACTATGTATTGCTCCTTTGCTCATTCAAGGAACAGCTGCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAAC
upper sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 1
attgtaaaatggattttttttcgtattttttttatgtggagaagtttg-ttggatgtagtacatttatggttttgatgtttcttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC
|||| | | | || | || | |||| | | | | | | || | || | || || || | || ||| |||||||||| ||| | || || || ||||| |||||| | || |||||||| || || ||||||||||||||||| |||| ||| |||||| | || |
tttgtctaggattccgtacatagttaacatcttgcatcatctgttttggccaggtattcctgttctcagattctaatatgtcac-tgttttattattacagACGCACTATGTATTGCTCCTTTGCTCATTCAAGGAACAACTCCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttggatgtagtacatttatggttttgatgtttcttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC
ttttgat putative branch site (score: 4)
tacatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgtaaaatggattttttttcgtattttttttatgtggagaagtttgttggatgtagtacatttatggttttgatgtttcttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - tgtggag
- - - - - - - - - - - - - - - - - - - - - - - - -tggatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg