Sequence
atgc intronic sequence ATGC exonic sequence...caaaattgcctccttgatagtggtttattataagataaacccttccctgcccctatgttgttcttgttctgctgctgattagttttattattttgaccagAATTCAGTGAATGCACGTTACCAGACCATTCCTTACCCTTGGTTGGTTTTTGGTGAGAAAGTTAAGGTCAATGCTGTTTTCATCCGTGATTCCACTGGTG
Basic information
species | Glycine max |
transcript | GLYMA15G29910.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G29910.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os03g53760.1 (Oryza sativa), 3'ss of exon 16
----------------------------------------------------------------caaaattgcctccttgatagtg-gtttattataagataaacccttccctgcccctatgttgttcttgttctgctgctgattagttt---tattattttga-ccagAATTCAGTGAATGCACGTTACCAGACCATTCCTTACCCTTGGTTGGTTTTTGGTGAGAAAGTTAAGGTCAATGCTGTTTTCATCCGTGATTCCACTGGTG
| || | | ||||| | || | || | | || | | | | | || |||||||| ||| | ||| | |||||||||||||||||| ||||||||||| ||||| || ||| |||| ||||||||||| || ||||| |||||||| ||||||||||| || || || |
gtaagttcatactggaacgtcttgaagttttcatgtgcaacaccctgcttactagcttatcacttgacctttcatgggagatagcccatctagggtgccatgtatagtgccttacatttcacagataccaaaattg-tgctgatttatttgcattttacgctattccagAATTCAGTGAATGCTAAGTACCAGACCATCCCTTATCCATGGCTGGTCTTTGGTGAGAAGGTGAAGGTAAATGCTGTCTTCATCCGTGACTCAACCGGAG
upper sequence: GLYMA15G29910.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G802858_T01 (Zea mays), 3'ss of exon 9
---------------------------------------------------------------------------------------caaaattgcctccttgatagtggtttattataagat-aaacccttccctgcccctatgttgttcttgttctgctgct--gattagttttattattttga---ccagAATTCAGTGAATGCACGTTACCAGACCATTCCTTACCCTTGGTTGGTTTTTGGTGAGAAAGTTAAGGTCAATGCTGTTTTCATCCGTGATTCCACTGGTG-------
| || | | | | | | ||| | | | |||| | | | || | || | || || | | ||| | |||||| | | |||||||||||||||||| || |||||||| || || || ||| |||| ||||||||||| || ||||| |||||||| |||||||||||||| || || |
gtaagtgcatagcagaatgtcctgaaatgttcgtatgcaatgccttgtttagtatctagctatctaatcacccctgctatcatatgctatgatacctttcaagttggcaagcgattccatgcttaaacacctactgataccaaagtagcactgatttctaagtttgaattcctgacattattcttaaattcagaattcagTGAATGCAAAATATCAGACCATCCCATATCCATGGCTGGTCTTTGGTGAGAAGGTGAAGGTGAATGCTGTCTTCATCCGTGATTCAACCGGAGTATCAGA
upper sequence: GLYMA15G29910.1 (Glycine max), 3'ss of exon 18
lower sequence: AT5G04895.1 (Arabidopsis thaliana), 3'ss of exon 16
caaaattgcctccttgatagtggtttattataagataaacccttccctgcccctatgttgttcttgttctgctgctgattagttttattattttgac----cagAATTCAGTGAATGCACGTTACCAGACCATTCCTTACCCTTGGTTGGTTTTTGGTGAGAAAGTTAAGGTCAATGCTGTTTTCATCCGTGATTCCACTGGTG
| | ||| || | || | | || || | ||| | | | || | | | || | | || ||||| ||| | |||||||| || ||| | || | || || ||||| ||||||||| | || ||||| |||||||| ||||||||||| || |||| || || ||||||||||
----gtgagcctcttcat--tcgtatttcccaacatcattacttgagtctctcgatatggccatcttttttatttaaatggtttttacggtttctatgtttcagAATTCTGTTAATTCGCGGTTCCCAACAATTCCATACCCTTGGCTAGTCTTTGGAGAGAAAGTAAAGGTCAATGCGGTACTCATACGGGACTCCACTGGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgcccctatgttgttcttgttctgctgctgattagttttattattttgaccagAATTCAGTGAATGCACGTTACCAGACCATTCCTTACCCTTGGTTGGTTTTTGGTGAGAAAGTTAAGGTCAATGCTGTTTTCATCCGTGATTCCACTGGTG
tgctgat putative branch site (score: 3)
ttatttt putative PPT
tgattagttttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaaattgcctccttgatagtggtttattataagataaacccttccctgcccctatgttgttcttgttctgctgctgattagttttattattttgaccagAATTCAGTGAATGCACGTTACCAGACCATTCCTTACCCTTGGTTGGTTTTTGGTGAGAAAGTTAAGGTCAATGCTGTTTTCATCCGTGATTCCACTGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - cctcctt
- - - - - - - -gatagtg
- - - - - - - - - - - - - - - - -gataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctgc