Sequence
atgc intronic sequence ATGC exonic sequence...gtacttttagacaatatcatatatatttttttttgtgtaatctagaataaatattttttgtttttctaatatatccatcaactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCCCAGCTGGTT
Basic information
species | Glycine max |
transcript | GLYMA0048S00340.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 6
gtactttta-gacaatatcatatatatttttttttgtgtaatctagaataaatattttttgtttttctaatatatccatcaactctgattc-tgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCCCAGCTGGTT
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ctgctctagcggtgatattatgt-tattaccaagagctagcttctcatcataaaatgcatattatgtttgc-tctcaacttatgctgattaacaatgtgcagATTTTTAAGGCCCCTTGTTGCCGATGTAGCTGTTGTTGCTAAGTGTCACTTAAGTGCACTGTATACCCATGAAAAGGGGCGTCTTTTTGCGCAGTTGGTT
upper sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G410479_T01 (Zea mays), 3'ss of exon 8
gtacttttagacaatatc-atatatatttttttttgtgtaatctagaataaatattttttgtttttctaatatatccatcaactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCCCAGCTGGTT
| | ||| | | | | | | || | | ||| | || || ||| | | | | | | | ||| || | || || || | ||||||||| || || |||||||| ||||| |||||||| ||||| |||||||||||||| | ||||||||||| |||||||| ||| ||||
attcagttaaatatcgtttacaagtggcattgctaacaaaccttagcttgcat-ttgtttatgccttatctttgcctacttatgctggttataatctgcagATTTTTGAGGCCCCTGGTTGCTGATGTTGCTGTTGTTGCCAAGTGCCACTTAAGTGCACTCTACACTCATGAAAAGGGACGGCTTTTTGCACAGTTGGTC
upper sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 6
-gtacttttagacaatatcatatatatttttttttgtgtaatctagaataaatattttttgtttttctaatatatccatcaactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCCCAGCTGGTT
| | | | | | || || || | | ||| ||| |||| || || | | | | || | | | | || ||| |||| ||| |||| | ||||| ||||| ||||||||||||||||| ||||| || |||| ||||||||||||||||| ||||| || |||||
tgcaatgatcaagggatgcttactgtccttcttctcccttctctctcttaa-tattcaggtttcttttggttttttattcctttttctcattttcatacagATATCTGAGACCTATTGTATCGGATGTGGCTGTGGTTGCCAAATGCCATTTGAGTGCTCTTTATACTCATGAAAAGGGGAAACTCTTTGCACAATTGGTT
upper sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 6
----gtacttttagacaatatcatatatatttttttttgtgtaatctagaataaatattttttgtttttctaatatatccatcaactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCCCAGCTGGTT
| | | | | |||| | | | |||| | ||| ||| | | || ||| | ||| ||| | || || ||| |||| ||| |||| | ||||| ||||||||||||||||| ||||| ||||| || |||| ||||||||||||||||| ||||| || |||||
cacaatgatcaagggatgcttgctgccctccttttcccttctctttcttaatagtcaggtttgttttgttttttaattccttt--ttctcattttcat--acagATATCTGAGACCTATTGTATCAGATGTGGCTGTAGTTGCCAAATGTCATTTGAGTGCTCTTTATACTCATGAAAAGGGGAAACTCTTTGCACAATTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataaatattttttgtttttctaatatatccatcaactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCCCAGCTGGTT
atattttttgtttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttttagacaatatcatatatatttttttttgtgtaatctagaataaatattttttgtttttctaatatatccatcaactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCCCAGCTGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - ttttgtg
- - - - - - - - - - - - - - - - - - - - - -agaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc