Sequence
atgc intronic sequence ATGC exonic sequencegtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA20G35110.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
|| || ||| || ||||| || | | || ||| | || | || || | || || | || | || |||||||| || ||||| || |||||||||||| ||||||| ||||| || || ||||| ||||| || ||| ||||| ||||||
--------------------gtaagcatcgtttacataaatatctcgtg-----ccatggacctcttgagtttgcagta----aagaaatt------gaataatttcaac-tatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttct-gatgagattgtggtaatgtttcc----agGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
| | |||| ||| | | |||||| | ||||| | | | |||| | ||| | || | | | | | | |||||||| || || ||||| |||||||||||| | ||||||| ||| || ||||||||||| || |||||| ||||||||||||
--------------------------gtaggtgcagcaaatctgttgggtcttgttctgttttgtt--tcttcaactcaaaatacattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 7
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgt--tctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
| || | | | | | | ||||| | | | ||| | | | | |||| | | || || | | | ||| |||||||| || || || || |||||||||||| | ||||||| ||||||||||||||||||||| |||||| |||||||| |||
-----------------------------gtaggtgaagccaacct--attcctatttgtggtctttgatttctt-tggtgtaaataaataatatgggtgaataatcttgagattt--agGTGGTCTCTTGGCGCCATTATGTATGAAATGCTTGTGGGGTTTCCGCCCTTTTATTCAGATGACCCAATGACAACTTGTAGGAAG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 6
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
|| | | |||| | | | | ||| | | || | | | | |||| || | || | ||| ||| | ||||||||||| || || || || ||||| |||||| | ||||| ||||| || ||||||||||||||||| ||| |||||||| |||
------------------------gttggttctctaaaactgtcatcatcttctatgatctgttttccccatggattagtttcctcatataaccatctgtttg----aatttctccagGTGGTCTCTTGGTGCTATCATGTACGAAATGCTTGTGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
| | ||| ||| ||||| | | | ||||| || || | |||||||| || ||||| |||||||| || ||| |||| |||||||||||||| ||||| || ||||| |||| ||||| | |||
-----------------------------------------------------------gtaagaggcatttctgattgaa--aatatctaccggcttgattgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 6
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
| ||||| ||| ||||| | | | ||||| || || | |||||||| || ||||| |||||||| || ||| |||| |||||||||||||| ||||| || ||||| |||| ||||| | |||
-----------------------------------------------------------gtaagaggcacttctgattgaa--aatatctaccggcttgattgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
tgtttcc CT-rich tract
ttcatattatttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG