Sequence
atgc intronic sequence ATGC exonic sequence...agtggtaatgaattttctttttgtcaacagttttaagtattaagtaatgcatgcatcatctccctttcactgactgtttgctccttttaaatgttttcagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
Basic information
species | Glycine max |
transcript | GLYMA16G00440.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g07194.2 (Oryza sativa), 3'ss of exon 2
agtggtaatgaattttctttttgtcaacagttttaagtattaagtaatgcatgcatcatctccctttcactgactgtttgctc----cttttaaatgtttt-cagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
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-ttcctcttcagctgtcat---ggaagccgctttaagtcgcagagtataattacatc-tataaaaggtaatatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
upper sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G435034_T01 (Zea mays), 3'ss of exon 1
-----------agtggtaatgaattttctttttgtcaacagttttaagtattaagtaatgcatgcatcatctccctttcactgactgtttgctccttttaaatgttttcagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
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gcatctacatccatgaaaactattagtgctcatatcatgtgtttacaatgctgagaaaagccag--ttagccacctttctcaaattatga---------aacatttttcagATGTCTGAGCAATTCAACCAGGAGCTATCATTGTCTGGGAAAATTCCATCTGGCTTCTTCAATACTATGTTTGAGTTTTCTGGCAGCTGGCAGAAAGATG
upper sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------------agtggtaatgaattttctttttgtcaacagttttaagtattaagtaatgcatgcatcatctc-----cctt--tcactgactgtttgct----ccttttaaatgtttt--cagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
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gtaacttttcgttgaaaagtattggtttgtgttgttgtaggttttgagtggataagatcgccatctgttgaagcctttatctagtttcct--tgtacattgttctagagagtaaatttccttcatagcattttggatgccttagttattaacattttgttaacatttttcttatggtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCAGGTCTCTTCAATGCCATGTTTGAATTCTCGAGCTGTTGGCAGAAAGACG
upper sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g01040.t01 (Vitis vinifera), 3'ss of exon 2
---agtggtaatgaattttctttt--tgtcaacagttttaagtattaagtaatgcatgcatc-atctccctttcactgactgtttgctccttttaaatgttttcagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
| | | |||| | ||| | | | |||||| | | | ||| || || | || ||| | ||| | ||| | |||||||||||||||||||| |||||| |||| |||||||| || ||||| ||||| || |||||| | |||||||||||||| || ||||||| | |||||
ttgttttacagttaattctaggacaatgttgatgctgtagcatattaaattcctctttcattgatttcgggtgcattga-tatttctttactttg-----ctccagATGTCAGAGCAATTCAACCAGGAGATATCCTTGACTGGTAAAATTCCATCAGGCCTCTTCAATGCTATGTTTGAATTTTCAGGCTGTTGGCAGAAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgcatgcatcatctccctttcactgactgtttgctccttttaaatgttttcagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
cactgac putative branch site (score: 2)
tgttttc putative PPT
ttttaaatgttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtggtaatgaattttctttttgtcaacagttttaagtattaagtaatgcatgcatcatctccctttcactgactgtttgctccttttaaatgttttcagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - -tgtcaac
- - - - - - - - - - - - - - - - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctcct