Sequence
atgc intronic sequence ATGC exonic sequence...tgcaacttttttgccagtacacacttctgcaccactttgtcaatgcttctatttccccctaggatgaatattctctaatctttacaattgtttttatcagTGGTCTGACAAGCTCCAGAAGCTTGATTTCCAAGAGATGGTAATGTTCCTTCAGCACCTTCCAACTAAGAACTGGACTCAACAGGAGCTCGAGATGGTAC
Basic information
species | Glycine max |
transcript | GLYMA15G03200.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G03200.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------------tgcaacttttttgccagtacacact-tctgcaccactttgtcaatgcttctatttccccctaggatgaatattctctaatctttacaattgttttta--tcagTGGTCTGACAAGCTCCAGAAGCTTGATTTCCAAGAGATGGTAATGTTCCTTCAGCACCTTCCAACTAAGAACTGGACTCAACAGGAGCTCGAGATGGTAC
|||| | ||| | | | | | | ||| | || || || | | | | | | | | | | | | || ||| || ||||||||| |||||||| |||| |||||||| ||||||||||| |||||||||||||||||||| || | ||||||| |||| || ||||| |||||||| |
gtaagttgaagtaccccttgactgttcataattatttttttcaacttcagtgtatgcaagtgttgcatgcctggtgcaggcaaatgcagttttcacaatgtttctggtgtaaatactaatgtccaagtccattgtaattaagttctctct-ttatttctacctcagTGGTCAGACAAGCTGAAGAAACTTGATTTTCAAGAGATGGTCATGTTCCTTCAGCACCTTCCGACGAGGAACTGGGCTCACCATGAGCTTGAGATGGTGC
upper sequence: GLYMA15G03200.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G142806_T01 (Zea mays), 3'ss of exon 10
---------------------------tgcaacttttttgccagtaca----cacttctgcaccactttgtc---aatgctt-ctatttccccctaggatgaatattctctaatctttacaattgtttttatc------agTGGTCTGACAAGCTCCAGAAGCTTGATTTCCAAGAGATGGTAATGTTCCTTCAGCACCTTCCAACTAAGAACTGGACTCAACAGGAGCTCGAGATGGTAC
|| | |||||| || || || | || || | |||| |||||| | | || | || ||| | || || | || | | | || ||||||| |||||||| |||||||| ||||| ||||||||||| |||||||| |||||||| || || | || |||| | || || ||||| |||||||| |
gtaagtcgctcctgtgaatgatgctaatgttaatttttttcccgtttgttattacaccaacaacaatctgtctgccatgcttgcaacttgcttgtaccgatgatagtttcaaaccctttcctctcccctcctctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC
upper sequence: GLYMA15G03200.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
---tgcaacttttttgcc-agtacacacttctgcaccactttgtcaatgcttctatttcccc-ctaggatgaatattctctaatctttacaattgtttttatcagTGGTCTGACAAGCTCCAGAAGCTTGATTTCCAAGAGATGGTAATGTTCCTTCAGCACCTTCCAACTAAGAACTGGACTCAACAGGAGCTCGAGATGGTAC
|||| | | | || | |||| | ||| |||| || | | | | || | | | | | || | | | ||||||||||| |||| ||||||| ||||| ||||| |||||||||||||| || |||||||| || | |||||| | | || |||||||| |||||
gtaagcaaacactgaatcgaatata-acttgcgt-tggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatg-cagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
upper sequence: GLYMA15G03200.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 9
----tgcaacttttttgccagtacacacttctgcaccacttt--gtcaatgcttctatttccccctaggatgaatattctctaatctttacaattgtttttatcagTGGTCTGACAAGCTCCAGAAGCTTGATTTCCAAGAGATGGTAATGTTCCTTCAGCACCTTCCAACTAAGAACTGGACTCAACAGGAGCTCGAGATGGTAC
|| |||||| | | | | | ||||| | | | | || | || | | | || | ||| |||||| ||||||||| || | ||| ||||||||||||||||||||| |||||||||||||||| |||||||||||| | ||||||||||| || |||||||||||||| |
tgtttgtgttttttttccttg-agatttctttgcacaattagaagctagattaagcatgaaacacttaaccatgtgtacactgttttttgt--ttgttt---tcagTGGTCGGATACGCTTCAGAAGCTTGATTTCCAAGAGCTGGTAATGTTCCTTCAACACCTTCCAACTCATAACTGGACTCACCAAGAGCTCGAGATGGTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctatttccccctaggatgaatattctctaatctttacaattgtttttatcagTGGTCTGACAAGCTCCAGAAGCTTGATTTCCAAGAGATGGTAATGTTCCTTCAGCACCTTCCAACTAAGAACTGGACTCAACAGGAGCTCGAGATGGTAC
ctctaat putative branch site (score: 3)
ttgttttt putative PPT
taatctttacaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcaacttttttgccagtacacacttctgcaccactttgtcaatgcttctatttccccctaggatgaatattctctaatctttacaattgtttttatcagTGGTCTGACAAGCTCCAGAAGCTTGATTTCCAAGAGATGGTAATGTTCCTTCAGCACCTTCCAACTAAGAACTGGACTCAACAGGAGCTCGAGATGGTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
tgcaact
- - - - ttttgcc
- - - - - - - - -tacacac
- - - - - - - - - - - - - - gcaccac