Sequence
atgc intronic sequence ATGC exonic sequence...ctttaatcaatatatgtgatgtttcctcttcaatatccaattaaaatcggatcagttcatattatgaattctagtctcagtaatggatttttggttgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
Basic information
species | Glycine max |
transcript | GLYMA16G09330.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 5
ctttaatcaatatatgtgatgtttcctcttcaatatccaattaaaatcggatcagttcatatta-tgaattctagtctcagtaatgg-atttttg-gttgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
| | | ||||| || | | ||| | | ||| | ||| ||| | || | | | || || |||||| || ||| |||||||| || ||||| ||||| ||||| ||||| ||||| || || ||||| || || || || |||||||| || ||||| ||||| ||||||||||| |||||
cacca--tattatattgtctgcatgtttgtcagttttcaagtcaaaatatatct-tccaggtagctttctgcttacctacctaatggtgttgttgtgttgcagGCAAGAAGGTGAGCAAGGCTCCTAAGATCCAGCGTCTTGTGACTCCCCTCACCCTCCAGAGGAAGCGTGCCAGAATCGCTGACAAGAAGAAGAGGATCGC
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
--ctttaatcaatatatgtgatgtttcctcttcaatatccaattaaaatcggatcagttcatattatgaattctagtctcagtaatggatttttggttgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
|| | | ||| ||| | | | | | || | | | | | | | | | | || | | | || | || |||| || ||||| ||||| || || ||||| ||||| || || || || |||| || || |||||||| || ||||||||||| ||||||||||| |||||
ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttcct--tttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
ctttaatcaatatatgtgatgtttcctcttcaatatccaattaaaatcggat-cagttcatattatgaattctagtctcagtaatggatttttggt-tgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
|| ||| | || | | | | | | ||| | | | ||| ||| || || | || | ||| || | |||||| || ||||| ||||| ||||| ||||| ||| | || || |||||| |||| || || |||||| | || ||||||||||| |||||||||||||||||
--acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 5
ctttaatcaatatatgtgatgtttcctcttcaatatccaattaaaatcggatcagttcatattatgaatt-ctagtctcagtaatggatttttggttgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
|| | | | ||| || | |||| ||| | | | | | | | |||| || ||| | || | || |||||| || ||||| ||||| ||||| ||||| ||| | || || |||||| |||| || || |||||| | || ||||||||||| |||||||||||||||||
---------gtaagaaaattagattcacttaaagagataattgaaaactgttta-tacgattgatgatttactaat----atatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 5
ctttaatcaatatatgtgatgtttcctcttcaatatccaattaaaatcggatcagttcatattatgaattctagtctcagtaatgg----atttttgg---ttgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
| ||| | || || || || || || | | | | | ||||| | | || | | ||| || | || | ||||| || ||| || |||||||| || || ||| | || || ||||| |||| ||||||||||||||||||||||||| || ||||| |||||||| ||
---------gttggtgttctaatttcttttttgatgggaaatatgatatgttta-ctgacattatttactaaagatgtatgattggtcttatctgtgtgcctggcagGTAAGAAGTGCAGTAAAGCTCCCAAAATACAGAGGCTGGTGACTCCCTTGACTTTGCAAAGGAAGCGGGCAAGAATTGCAGAGAAGAAAAAGAGAATTGC
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 5
-ctttaatcaat---atatgtgatgtttcctcttcaatatccaa--ttaaaatcggatcagttcatattatgaattctagtctcagtaatggatttttggttgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
|| ||| || || | | | |||| ||| || || | | | || | || || | || ||| | || | | ||||||| || || ||||| || ||||||||| | || || || ||| |||| ||||| |||||||| ||||| ||||| || |||||||||||||| ||
actgaaattcatgtgatgcttaaaagtattatttcagtattttgctttttaaaagactaaagacagaagattgata-tggtttcatcactgtgatcct-----cagGGAAGAAATGCAGTAAAGCCCCTAAGATTCAGAGGCTGGTGACCCCATTGACTCTGCAGAGGAAGCGTGCAAGGATTGCAGAGAAGAAGAAGAGAATTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcggatcagttcatattatgaattctagtctcagtaatggatttttggttgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
ttttt CT-rich tract
ttcatattatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttaatcaatatatgtgatgtttcctcttcaatatccaattaaaatcggatcagttcatattatgaattctagtctcagtaatggatttttggttgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - tgatgtt
- - - - - - - - - - - - cctcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaattc