Sequence
atgc intronic sequence ATGC exonic sequence...aaaaaaaaaaaacttactgtattgtgatgtaatagtttgtacaaagccaaggtattgaatctctgattttctctacattcctgatcctgtattggtgcagACCATTTTGGTTGAACCAACAACTGGAAATACGGGACTTGGCATTGCTTTTGTTGCAGCAACAAAGGGGTACAAACTTATAGTCACAATGCCAGCTTCTG
Basic information
species | Glycine max |
transcript | GLYMA03G00900.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G00900.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g59920.1 (Oryza sativa), 3'ss of exon 3
aaaaaaaaaaaacttactgtattgtgatgtaatagtttgtacaaagccaaggtattgaatctctgattttctctacattcctgatcctgtattggtgcagACCATTTTGGTTGAACCAACAACTGGAAATACGGGACTTGGCATTGCTTTTGTTGCAGCAACAAAGGGGTACAAACTTATAGTCACAATGCCAGCTTCTG
| ||| | || ||||| | | ||| | | | |||| | | || | | || | | ||| | |||||||||||||||||||||||| ||||||||||| || | ||| | |||| ||| || || | | ||| ||||| || |||| || | || | ||
---------------gttagattatcctg--atagtatttgcaatactaccatcatgaagattctaacttgtgcatatacttctacctat------gcagACCATTTTGGTTGAACCAACTACTGGAAATACTGGTATAGGCCTAGCTTCTGTGGCTGCTGCTAGGGGATACAAGCTAATAGCAACTGTACCTTCATCAA
upper sequence: GLYMA03G00900.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G133359_T01 (Zea mays), 3'ss of exon 3
aaaaaaaaaaaacttactgtattgtgatgtaatagtttgtacaaagccaaggtattgaatctctgattttctctacattcctgatcctgtattggtgcagACCATTTTGGTTGAACCAACAACTGGAAATACGGGACTTGGCATTGCTTTTGTTGCAGCAACAAAGGGGTACAAACTTATAGTCACAATGCCAGCTTCTG
||| | | | | || | | | |||| | | | || ||| | || | ||| | ||||| | ||||||||||||||||| |||||||||||||||||||| || | | |||||||| ||| || ||| ||| || ||||| | |||| |||||||| | ||
---gttaaagaccatctcatgttatta-gcaatattatcatcgcctacattgtaatatatg-cagatggtttctacct----------------gtgcagACCATTTTGGTAGAACCAACAACTGGAAATACTGGTGTAGCCATTGCTTCTGTGGCTGCAGCAAGAGGATACAAGTTGATAGCAACAATGCCTTCATCGT
upper sequence: GLYMA03G00900.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G03630.1 (Arabidopsis thaliana), 3'ss of exon 3
aaaaaaaaaaaacttactgtattgtgatgtaatagtttgtacaaagccaaggtattgaatctctgattttctctacattcctgatcctgtattggtgcagACCATTTTGGTTGAACCAACAACTGGAAATACGGGACTTGGCATTGCTTTTGTTGCAGCAACAAAGGGGTACAAACTTATAGTCACAATGCCAGCTTCTG
||| |||| | | || | | | || || ||| | || | ||| | || | | ||| |||||| | || || ||||||||||| ||||| || || ||||| ||||| ||||| || ||| | || || ||||| |||||||| |||||||||||||||
------------gttattgtact-tcttgcctttcgatattttaatgttctgtgttgccacattgtagattgctaattcgatggtgtt--attaaagcagACTGTATTAGTAGAACCAACAACCGGAAACACTGGCCTTGGGATTGCATTTGTGGCTGCAGCTAAAGGCTACAAGCTTATAGTGACAATGCCAGCTTCTA
upper sequence: GLYMA03G00900.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0056g00820.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------aaaaaaaaaaaacttactgtattgtgatgtaatagtttgtacaaagccaaggtattgaatctctgattttctc-tacattcctgatcctgtattggtgcagACCATTTTGGTTGAACCAACAACTGGAAATACGGGACTTGGCATTGCTTTTGTTGCAGCAACAAAGGGGTACAAACTTATAGTCACAATGCCAGCTTCTG
| |||| || || |||| | | || | | | | | ||| | | | || || | | |||| || |||||| || || ||||||||||||| ||| ||||| |||||||| ||||| |||||||| || || ||||| ||||||||||||||||| ||||| || ||
gtaagcttcttctcttgaacttatggaaatggcactctttagatcaatatctattgttattactgaaaaccccttttctctattaattgggattaatcactgaagcctggtgaaagcatgtctttagtaccattgtatatctcgttttctgtctttatgcagAGTATATTAGTTGAACCAACAAGTGGTAATACAGGACTTGGTATTGCATTTGTTGCGGCCACTAAGGGATACAAACTTATAGTCACCATGCCTGCATCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccaaggtattgaatctctgattttctctacattcctgatcctgtattggtgcagACCATTTTGGTTGAACCAACAACTGGAAATACGGGACTTGGCATTGCTTTTGTTGCAGCAACAAAGGGGTACAAACTTATAGTCACAATGCCAGCTTCTG
tcctgat putative branch site (score: 3)
tattgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaaaaaaaaacttactgtattgtgatgtaatagtttgtacaaagccaaggtattgaatctctgattttctctacattcctgatcctgtattggtgcagACCATTTTGGTTGAACCAACAACTGGAAATACGGGACTTGGCATTGCTTTTGTTGCAGCAACAAAGGGGTACAAACTTATAGTCACAATGCCAGCTTCTG
aaaaaaa
- - - - - - cttactg
- - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - - -caaagcc