Sequence
atgc intronic sequence ATGC exonic sequence...ttgacatttatgttatacatttatactttctgtagttggttgattttatcatatttcgttgtctggtaagtaacatacaatttttaattgggcaatgcagTTTATGAAAGGTATACCAAAATTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTG
Basic information
species | Glycine max |
transcript | GLYMA07G36340.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
--------------ttgacatttatgtt---atacatttatactttctgtagttggttgattttatcatatttcgttgtctggtaagtaacat------acaatttttaattgggcaatg--cagTTTATGAAAGGTATACCAAAATTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTG
|| || ||||| ||| | | | | | | | | ||| || | || | |||| || ||||| | ||| | ||| || | | | |||| ||||| ||||||||||||||||| ||| |||| || | ||||||||||| || | |||||| ||| |||||||||||
gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattacc--acaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 3
ttgacatttatgttat--acatttatactttctgtagttggttgattttatcatatttcgttgtctggtaagtaacatacaatttttaattgggcaat--gcagTTTATGAAAGGTATACCAAAATTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTG
| | || | | | | | | || ||| |||| || |||| | | | | ||||| | ||| | ||| || | | | |||| ||||| ||||||||||||||||| ||| |||| || | ||||||||||| || | |||||| ||| |||||||||||
---ataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttct-caattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------------------------------------ttgacatttatgttatacatttatactttctgtagttggttgattttatcatatttcgttgtctggtaagtaacatacaatttttaattgggcaatgcagTTTATGAAAGGTATACCAAAATTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTG
| ||| || || | ||||| | || | | | ||| ||| || ||| || | | ||| | |||| ||| || | |||||||||||||| ||||| ||||| || |||||||||||||| ||||| | || ||||||||||| || ||||| ||| ||||||| | |
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctctta--ttctgttttttttctgtttgg--aatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 2
ttgacatttatgttatacatttatactttctgtagttggttgattttatcatatttcgttgtctggtaagtaacatacaatttttaa---ttgggcaatgcagTTTATGAAAGGTATACCAAAATTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTG
| | | | || | ||||| ||| ||| | | || || | || | || | | || | | | |||||| ||| | ||||||| | |||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||| || |||||||| |||| |||||| | |
-taataatataattttgcattt-tacaatctttgtgttactggagttgtttcatctgatt-tattttattttatgttttatttttgtactttgataagagcagTTTTTAGGAGGTATACCAAAGTTTGTGAAGATAGTGGAAGTTGGTCCAAGGGATGGATTGCAAAATGAGAAGAATATTGTACCTACAGCTGTAAAAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcatatttcgttgtctggtaagtaacatacaatttttaattgggcaatgcagTTTATGAAAGGTATACCAAAATTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTG
taagtaacatacaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgacatttatgttatacatttatactttctgtagttggttgattttatcatatttcgttgtctggtaagtaacatacaatttttaattgggcaatgcagTTTATGAAAGGTATACCAAAATTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - -ctttctg
- - - - - - - - - - - - - - - - - gttggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acataca