Sequence
atgc intronic sequence ATGC exonic sequence...actgctacctaggttatttcagttacttattaaaaggtgtcatgattctattaagcttctccgaaagtgtgtgtgtctaactatgttcaatatgatgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
Basic information
species | Glycine max |
transcript | GLYMA06G33380.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 6
actgctacctaggttatttcagttacttattaaaaggtgtcatgattctattaagcttctccgaaagtgtgtgtgtctaactatgttcaatatgatgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
||| | | | ||| | | ||| | || | | | | || | | || | ||| || | | | |||| ||||||||||| || ||||| || ||||| || || ||| | || ||||||||||||||||||||||| ||||| | ||||||||| |||| |||||
-------------gtatgtta--catctatcatatcatgtttgcaacatagttaattaattgtgaaat-tatggttttaatattgat--gtggactacagGAAATCCAAGAGTCACACCAGAGGTTACAAGGGACGTATGCCTGTTAGCTAGAATGATGGCTGCTAACTTATACTATGCACAGATAGAGGATCTGATGTT
upper sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
actgctacctaggttatttcagttacttattaaaaggtgtcatgattctattaagcttctccgaaagtgtgtgtgtctaactatgttcaata---tgatgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
|| | | || | |||| | || ||| ||| | | ||| | ||| || | || ||| ||||||||||| || |||||||| ||||| ||||| ||||| | ||||||||||||||| | || || |||| ||| || || ||| |||| |||||
----------------------gtatgcaaaggatggcttttgacttctgtatag-ttcagttcttgtgcatttaa-taattttgtgcattgcaccaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
upper sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
--------actgctacctaggttatttcagttacttattaaaag-gtgtcatgattctattaagcttctcc--gaaagtgtgtgtgtctaactatgt-tcaatatg-atg-cagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
| || || |||||| | |||| | | | || || | | | ||| | || ||| | ||||| || || | ||| |||| ||||||||||| || ||||| || ||||| ||||| ||||| ||||||||||||||||||||||| ||||| | |||||||||| | || |||||
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
upper sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------actgctacctaggttatttcagttacttattaaaaggtgtcatgattctattaagcttctccgaaagtgtgtgtgtctaactatgtt-caatat-------gatgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
|| || || |||| | ||| || | | | | ||| | | | | | | |||| | | | |||| | ||||||| ||||||||||| || ||||| || || || ||||| ||||| | || ||||||||||| | |||||||||| ||| ||||| ||| |||| |||||
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
upper sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 4
-actgctacctaggttatttcagttacttattaaaaggtgtcatgattctattaagcttctccgaaagtgtgtgtgtctaac-tatgttcaatatga--tgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
| | || | | ||| |||| ||| |||| | | || || |||| | | | |||| | || | |||| |||||| || ||||| || ||||| || || ||||| |||||||||||||||||||||||||||||||||||||| ||||| |||||||||||| ||||||||||
taat-ttatcaaagttgagtcag--actcattagttgac-taccagttatagaaagcaggactctctctcccctggattaacatgcttttgacatgaaatgcagGTAACCCAAGGGTGACTCCTGAGGTCACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTATACTATTCCCAGATAGAGGATCTTATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctattaagcttctccgaaagtgtgtgtgtctaactatgttcaatatgatgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
gtctaac putative branch site (score: 2)
ttcaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgctacctaggttatttcagttacttattaaaaggtgtcatgattctattaagcttctccgaaagtgtgtgtgtctaactatgttcaatatgatgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- tgctacc
- - - - - - - - - - - - - - - - - - -tgtcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtg