Sequence
atgc intronic sequence ATGC exonic sequence...tatcttagaatgatttctaattggtcaagtgtatgaatataaatcatatacgtacaaaggataattcacagaaagcaacatttaattttgttcatggcagGACATTGAAAAGAAGAACATCCTGGCAGTGCAAACTCTTCGAAATCTGATAATGGGATCAACTCTTATGGCCACCACTTCCATTCTCCTCTCTGCAGGCT
Basic information
species | Glycine max |
transcript | GLYMA20G35780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g02760.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------------tatcttagaatgatttctaattggtcaa-gtgtatgaatataaatcatat--acgtacaaaggataattcacagaaagcaacatttaattttgttcatggcagGACATTGAAAAGAAGAACATCCTGGCAGTGCAAACTCTTCGAAATCTGATAATGGGATCAACTCTTATGGCCACCACTTCCATTCTCCTCT-CTGCAGGCT
||| | |||| ||||| || | | | | || || | | | | | || | | || ||| | ||| || ||||||||| || ||||||||||| ||||| ||||| |||||||||||| ||| ||||| || || || ||||| || || || || || || | ||| | |
gtactaaacactaatcacccccacctcatatttccttcttgtttgatcagaacttgatgcttaattagttatcacattgtccttttgattattttgatgattttggaagaaactataatgag-ggtgtttgaatttttt---ggcagGACAACGATAAGAAGAACATTCTGGCGGTGCAGACTCTTCGAAATGCGATCATGGGGTCGACCCTAATGGCAACTACATCAATCCTTCTGTGCTGTGGCC- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatacgtacaaaggataattcacagaaagcaacatttaattttgttcatggcagGACATTGAAAAGAAGAACATCCTGGCAGTGCAAACTCTTCGAAATCTGATAATGGGATCAACTCTTATGGCCACCACTTCCATTCTCCTCTCTGCAGGCT
atttaat putative branch site (score: 4)
ttttgttc CT-rich tract
aacatttaattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatcttagaatgatttctaattggtcaagtgtatgaatataaatcatatacgtacaaaggataattcacagaaagcaacatttaattttgttcatggcagGACATTGAAAAGAAGAACATCCTGGCAGTGCAAACTCTTCGAAATCTGATAATGGGATCAACTCTTATGGCCACCACTTCCATTCTCCTCTCTGCAGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - -tgtatga
- - - - - - - - - - - - - - - - - - - - - - catatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attcaca