Sequence
atgc intronic sequence ATGC exonic sequence...taacttatgaaattttggtccatttttattcttgttgatttcctagattgtccttgctagatgaattttaccaattacacttgtattaacaccttggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTATTTTTGGATGATGATGTTAGGTTACATCCTGGATCAATCGGAGCGCTCACTCGTGAGA
Basic information
species | Glycine max |
transcript | GLYMA05G35860.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G35860.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------------------------------taacttatgaaattttggtccatttttattcttgttgatttcctagattgtccttgctagatgaattttaccaattacacttgtat-taacaccttg-----gcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTATTTTTGGATGATGATGTTAGGTTACATCCTGGATCAATCGGAGCGCTCACTCGTGAGA
||| |||||| | || || | | |||| | | | | | || ||| | | | | ||| | | | ||| | || ||||||| || | |||||| ||||||| ||||||||| ||||||||||||||||||||||| | ||||||||| |||||||||| ||||| |||||
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaacc-atgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
upper sequence: GLYMA05G35860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 5
taacttatgaaattttggtccattt--ttattcttgttgatttcctagattgtccttgctagatgaattttaccaattacacttgtattaacaccttggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTATTTTTGGATGATGATGTTAGGTTACATCCTGGATCAATCGGAGCGCTCACTCGTGAGA
| || | | || ||| | | | || || |||| || | | || |||| || || | | || | | |||||||| ||||| | |||||||||||| ||||| ||||||||||| ||||||||||||| ||| | |||||||| | || || || ||| | |||||
atatttgtatacacctgttccctgtaatggttgaagtatttttctagaatcatgtagtttttttgtgctttatcatgtatattctggtt--ctctaatacagGTTGGGGTGGATAGAATGCATAAAGACAGCAAGTATGTATTATTCCTGGATGATGATGTCAGGCTGCATCCTGGGACCATTGGGGCCCTCGTTGCTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgtccttgctagatgaattttaccaattacacttgtattaacaccttggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTATTTTTGGATGATGATGTTAGGTTACATCCTGGATCAATCGGAGCGCTCACTCGTGAGA
tattaac putative branch site (score: 1)
aattttaccaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taacttatgaaattttggtccatttttattcttgttgatttcctagattgtccttgctagatgaattttaccaattacacttgtattaacaccttggcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTATTTTTGGATGATGATGTTAGGTTACATCCTGGATCAATCGGAGCGCTCACTCGTGAGA
- - - - - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttgt