Sequence
atgc intronic sequence ATGC exonic sequencegtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
Basic information
species | Glycine max |
transcript | GLYMA02G05440.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
| | | || |||| || | ||| ||| | | |||| | ||| | ||| || || | | || | | ||| ||| || ||| || | | || ||| ||||||||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||| || ||| | |||||||| ||||| || || ||
----------------------gtatttatttcaagagcttttgcttatgtgcatcttt-gctatgtgctt--ccaattgttgcttctgatttgagtaggaca----tacaagtctgcagttcattcattgttttctttc-----attactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgt----aattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
|| ||| | ||| | || | | ||| ||| || ||| | ||||| | || || || | | |||| ||| | |||| ||| |||||||| ||||| |||||||| ||||| |||||| | || || |||||||| || |||| || || ||||||||||| ||
-----------------------------------------------------------aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagttgccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
| | | | ||| | || | | || | | | | || | ||| | ||| ||||| | ||| | | | ||| || ||||| ||||| |||||||| |||||||||||||| ||||| ||||| ||||||| ||| |||||| | |||||||| ||||| || || ||
------------------------------------------------------gtatctacttggggccatctgaatctgtcggg--aatctgataggggcaagtctgcagttt-agctga---ccattttgtt--gtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatc-aagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
| | | ||| || || | ||||| || | | || || | | | || | || |||| ||| ||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| | ||| || ||| |||||||||||||||||||||||||
------------------------------------------------------------------------------gttagtagcaaagtgatttaaagtttttcttgacatatcactt----ctttgatctaaccat-tatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
| | || | || ||||| | || | || | || | || | |||| |||||| || ||||| ||||| || || || || ||||| ||||||||||||||||| ||||| | |||||| ||| ||||||| || ||||||||||||||
------------------------------------------------------------------------------gtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtagataatggaggtgattttgtgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 5
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
| |||| || | | |||||| | | | ||| | |||| ||| | || || || || | | ||| | ||||| | ||| | ||| | || | || ||| |||| || |||||||| ||||||||||| ||||| ||||||||||| |||||||| || | ||| || || || ||| |||||||||| ||||||||||||||
------gtaagtgaaatttcgccttctcaatatatggactttgaaat----ccatattt--tcatgggttt---ctgttgttcaaac--aattacaacatatgcttctagcttttgaattggaaaaa--------ctgaatatgaataaacacagGGAAGAAGTTTCAAGATATTGTTGGTAGTGCCTACTATGTTGCTCCTGAAGTATTGAGACGGAAATCGGGACCTGAATCAGATGTCTGGAGTATTGGTGT
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S199_57V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
| || | || ||||| |||| | || || || | ||| ||| | | | || || | || | ||| | | || || | | | | || | | | | | |||||||| || ||||| | || || || || ||||| || || || ||||| || || || ||||||||| |||| ||||||||||||||||||||
-----gtaacgctctgcttttcctgcttctggacatt-ttgaactctctttctctttctgggtttgggtttaatg-atgattagaattggttgcttgagttcactgct-tgccctcacctgtggcatgcctcttctt--------------gcagGAAATCGATTCCATGACGTAGTCGGAAGCGCGTACTACGTGGCTCCAGAAGTTTTGAAGAAAAAATCAGGTCCTGAATCTGATGTGTGGAGTATTGGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
taattttatttgagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG