Sequence
atgc intronic sequence ATGC exonic sequence...tcactcacaaattcaccccaaaaaatattttttttggcttgctgcttttaactgagtttgaaattaagcattgaatttatatttgaagaaacttgtgcagTACTTCTTATACCAGCTGTTACGGGGGCTTAAATATGTTCACTCGGCTAACGTTTTGCACCGTGACCTTAAGCCCAGTAACTTACTAATGAATGCAAACT
Basic information
species | Glycine max |
transcript | GLYMA08G02060.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G02060.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------tcactcacaaattcaccccaaaaaatat-tttttttggcttgctgcttttaactgagtttgaaatt-----aagcattgaattta--tatttgaagaaacttgt--------gcagTACTTCTTATACCAGCTGTTACGGGGGCTTAAATATGTTCACTCGGCTAACGTTTTGCACCGTGACCTTAAGCCCAGTAACTTACTAATGAATGCAAACT
|| ||| | | ||| | |||| | | || || | || || | ||| || |||| || ||| || ||| |||||||||| | |||||| || |||| ||||| |||||||| |||||||| || || ||||||||||| || ||||| || || || | | |||||||| |
gtttgttgcttccagcttgtgctttgctgaaacattttgcttgcagaaaatctagacagagatttccatgcaccttgttcctttggtcgctatatgttttcttcatcctatccatatttcagcttaacattctcttgtttatctggtttaataatcacaagtgacatgttttgcattgcagTACTTCCTGTACCAGTTGCTACGAGGGCTAAAATATGTGCACTCGGCAAATGTCTTGCACCGTGATCTGAAGCCAAGCAATTTGTTCCTTAATGCAAATT
upper sequence: GLYMA08G02060.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 3
tcactcacaaattcaccccaaaaaatattttttttggcttgctgcttt-taactgagtttgaaattaagcattgaatttatatttgaagaaacttg---tgcagTACTTCTTATACCAGCTGTTACGGGGGCTTAAATATGTTCACTCGGCTAACGTTTTGCACCGTGACCTTAAGCCCAGTAACTTACTAATGAATGCAAACT
|| | | | | | | ||||| ||| | | | || | |||| ||| | || ||||||||||||| || ||| ||||||| ||||| |||||||| ||||| || || | |||||||| || || ||||| || || || | | |||||||| |
----acaaagaactatattttggtacggagggagtaatatattgcttcacaacaatgatatattctataatctatatttctatgttccccctttttccttgcagTACTTCTTGTATCAGTTGTTACGAGGGCTAAAATATGTGCACTCAGCAAATATATTGCACCGCGATCTGAAGCCGAGCAATTTGTTCCTAAATGCAAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaactgagtttgaaattaagcattgaatttatatttgaagaaacttgtgcagTACTTCTTATACCAGCTGTTACGGGGGCTTAAATATGTTCACTCGGCTAACGTTTTGCACCGTGACCTTAAGCCCAGTAACTTACTAATGAATGCAAACT
ttttaac putative branch site (score: 2)
tttgaaattaagcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcactcacaaattcaccccaaaaaatattttttttggcttgctgcttttaactgagtttgaaattaagcattgaatttatatttgaagaaacttgtgcagTACTTCTTATACCAGCTGTTACGGGGGCTTAAATATGTTCACTCGGCTAACGTTTTGCACCGTGACCTTAAGCCCAGTAACTTACTAATGAATGCAAACT
-cactcac
- - - - - -ttcaccc
- - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaattaa