Sequence
atgc intronic sequence ATGC exonic sequence...aagaagccaccccagttagtggctagcatttccttggcaccacttttgtactactgtattattatacttactgaaaattctttactattttttattgcagCTATCAGCTTCAAAAGTACAAAAATGCTGGCTCATTTGTTCTTCCAGTGGATCCTAAGGACAAGGAAACTTGGGGTGATAGTGAACACAGGCTTGCATAT
Basic information
species | Glycine max |
transcript | GLYMA12G08140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08140.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G60700.1 (Arabidopsis thaliana), 3'ss of exon 1
aagaagccaccccagttagtggctagcatttccttggcacca--cttttgtactactgtattattatacttactgaaaattctttactattttttattgcagCTATCAGCTTCAAAAGTACAAAAATGCTGGCTCATTTGTTCTTCCAGTGGATCCTAAGGACAAGGAAACTTGGGGTGATAGTGAACACAGGCTTGCATAT
| || | | | || | | | | | |||| | || | || || | | | || ||| | | | || |||||| ||||||||||| || |||| |||||| || || ||||||||||| || ||||| || || ||||| |||||||| ||||||||||||||| | || |||
-aaaatagattcaaattctctggggaaaagttataaaaatggattttttttgttatgaagtaataattgtggttttgattttttttgtgtgtgtt-ttgcagTTATCAGCTTCAGAAATACAGAAATGCAGGTTCGTTTGTTCTTCCCGTTGATCCAAATGATAAGGAGACTTGGGGAGATAGTGAACACAGGTTAGCTTAT
upper sequence: GLYMA12G08140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g02690.t01 (Vitis vinifera), 3'ss of exon 1
aagaagccaccccagttagtggctagcatttccttggcaccacttttgtactactgtattattatacttactgaaaattctttactattttttattgcagCTATCAGCTTCAAAAGTACAAAAATGCTGGCTCATTTGTTCTTCCAGTGGATCCTAAGGACAAGGAAACTTGGGGTGATAGTGAACACAGGCTTGCATAT
|| ||| | ||| | | | || | ||| | || || | || || | || | | | | | ||||||||||||||||| ||||||| | ||||||||||||| |||||||| || ||||| || |||||||||||||||||||| ||||||||||||||||| |||
ctgatatttggatagtgacaggcagaatactgatgagtacttcctttatgactctaccttctgattctgcttctaatgattggaacctctaattgtgcagCTATCAGCTTCAGAAGTACAGAGATGCTGGCTCATTCGTTCTTCCTGTTGATCCAAATGACAAGGAAACTTGGGGTGACAGTGAACACAGGCTTGCTTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtactactgtattattatacttactgaaaattctttactattttttattgcagCTATCAGCTTCAAAAGTACAAAAATGCTGGCTCATTTGTTCTTCCAGTGGATCCTAAGGACAAGGAAACTTGGGGTGATAGTGAACACAGGCTTGCATAT
tacttac putative branch site (score: 1)
ttctttactatttttt putative PPT
tattattatacttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaagccaccccagttagtggctagcatttccttggcaccacttttgtactactgtattattatacttactgaaaattctttactattttttattgcagCTATCAGCTTCAAAAGTACAAAAATGCTGGCTCATTTGTTCTTCCAGTGGATCCTAAGGACAAGGAAACTTGGGGTGATAGTGAACACAGGCTTGCATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - ccacccc
- - - - - - - - - gtggcta
- - - - - - - - - - - - -gcatttc
- - - - - - - - - - - - - - - - - - gcaccac
- - - - - - - - - - - - - - - - - - - - - - - - -actactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttactg