Sequence
atgc intronic sequence ATGC exonic sequencegtaacaaacaagacatgttgatcataggttttcttgcatatttctttgaagttgattgaataaatccaaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
Basic information
species | Glycine max |
transcript | GLYMA16G02770.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 14
gtaacaaacaagacatgttgatcataggttttcttgcatatttctttgaagttgattgaataaatccaaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
| | || ||||| | ||| | | | | | ||| || | | || |||| | | ||| || ||| ||||||||| |||||||||||||| ||||||||||| || || || || || |||||||| | ||||||||||| ||||| ||||| || | ||||| || |
tcactagttttctgatattgattgaacttttgttaagacacagaat-ggagtaatttacaaatat---aactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaacaaacaagaca-tgttgatcataggttttcttgcatatttctttgaagttgattgaataaatc------caaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
||||| |||||||| | || | | || || | | | | | | |||| | | | |||| || | | || | | | |||||||||||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||||||||| ||||||||||
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagACTTTCTATTTTAAATCTATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG------------------------
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 16
gtaacaaacaagaca-tgttgatcataggttttcttgcatatttctttgaagttgattgaataaatc------caaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
||||| |||||||| | || | | || || | | | | | | |||| | | | |||| || | | || | | | |||||||||||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||||||||| ||||||||||| ||||||||||| ||||| || |
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagactttctattttaaatctatgcagCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGA
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 1
gtaacaaacaagacatgttgatc--------------ataggttttcttgcatatttctttgaagttgattgaataaatccaaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
|| | ||||| ||| | | | | || | | || || || | | ||| || | || | | | | | |||| | || | | || |||||||||||||||||||||||||||||| | || || ||||| ||||| ||||| || |||| |||||||| ||||| |||||||| | |||||| ||||
gtgatgaacaaactatgctatttgatagaagaatagaacacattgtttcttatcttgtcttacaaataattaaaccattcaataatctggatttaattgcatttctttttcttttcagCAAGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAACTATAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAA
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 16
gtaacaaacaagacatgttg---------atcatagg-----ttttcttgcatatttctttgaagttgattgaataaatccaaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
|| | ||||| ||| | || |||| || | | || || || | | ||| || | || | | | | | |||| | || | | || |||||||||||||||||||||||||||||| | || || ||||| ||||| ||||| ||| |||| |||||||| ||||| |||||||| | |||||| ||||
gtgatgaacaaactatgctatttgatagaataatagaacacattgtttcttatcttgtcttacaaataattaaaccattcaataatctggatttaattgcatttctttttcttttcagCAAGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAGCTCTAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgattgaataaatccaaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
tgctgat putative branch site (score: 3)
aaactttatacataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaaacaagacatgttgatcataggttttcttgcatatttctttgaagttgattgaataaatccaaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG