Sequence
atgc intronic sequence ATGC exonic sequence...gtgatctttgtcatgaaattatgatgctaagtgcaagtattttgttgagttcgcttgtttaagtataaagtttttttgtcatgatcttctggatgtggagAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCAGGAGTTATT
Basic information
species | Glycine max |
transcript | GLYMA05G07540.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G07540.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g49570.1 (Oryza sativa), 3'ss of exon 8
gtgatctttgtcatgaaattatgatgctaagtgca--agtattttgttgagttcgcttgtttaagtataaagtttttttgtcatgatcttctggatgtggagAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCAGGAGTTATT
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-------------gtaagttatgcttcagatttcaccaatttattagcagcagagtttcgttatgtattggttgttgttatt-tgaacta--gGATGTGGCGGGAAATTCGACTCCTAGCTGACACCAAGCCTGTGGTTGCTTCAATGTCTGATGTTGCTGCAAGTGGTGGGTACTACATGGCAATGGCTGCA---------
upper sequence: GLYMA05G07540.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G122843_T02 (Zea mays), 3'ss of exon 13
gtgatctttgtcatgaaatt--atgat--gctaagtgcaagtatt--ttgttgagttcgcttgtttaagtataaagtttttttgtcatgatcttctggatgtggagAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCAGGAGTTATT
|| | | | | | ||| |||| ||| || | | ||||| | | | ||| | | || || | | ||||||||||||||||| | ||||| || ||| ||||| || ||||||| ||||||||||| || |||||||| || |||||||||||||||| |||
gtaagttacgccttaggatttagtgatttgcttctcagcagcagcagcagcagagttttttcagtaacatattacgaattcttatttcaacta---gGATGTGGAGAGAAATCCGACTTCTAGCCAACTCTAAACCTGTAGTTGCTTCGATGTCTGATGTTGCTGCAAGTGGGGGCTACTACATGGCAATGGCTGCA---------
upper sequence: GLYMA05G07540.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
-gtgatctttgtcatgaaattatg-atg---ctaagtgcaagtattttgttgagttcgcttg-tttaagtataaagtt---tttttgtcatgatcttctggatgtggagAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCAGGAGTTATT
| | | | || | ||| || | | | || |||| | || | || | ||||| || | || | ||| | | | | |||||||| || |||| || ||||||| ||||||| |||||||| |||||||| |||||||||||||||||||| |||||||||||||||| |||
tatctatctagcctagaggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA---------
upper sequence: GLYMA05G07540.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g04690.t01 (Vitis vinifera), 3'ss of exon 4
----------gtgatctttgtcatgaaattatgat-gctaagtgcaagt--attttgttgagttcgc-ttgtttaagtataaagtttttttgtcatgatcttctggatgtggagAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCAGGAGTTATT
||| | | | ||| | | | || |||| | | | | |||| || | | || | || |||| | | ||| | | |||||||| |||||||| |||||||||||||||||||| |||||||| ||||||||||||||||| || || |||||||||||||||||||||||||||
gcttgtacagatgaaaaaagagaaggaatgagaaaagaaaaatgcatgacaaatataatgagctcccactaattggtccttaatttttatgattatg-----cagAATGTGGAGGGAAATCAGACTTCTGGCTGCCTCAAAACCTGTCATTGCATCAATGTCTGATGTGGCTGCTAGCGGAGGGTACTACATGGCAATGGGAGCA---------
upper sequence: GLYMA05G07540.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S25_21V6.1 (Physcomitrella patens), 3'ss of exon 11
----gtgatctttgtcatgaaattatgatgctaagtgcaagtattttgttga-gttcgcttgtttaag----tataaagtttttttgtcatgatcttctggatgtggagAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCAGGAGTTATT
| | | || | ||| | | |||||| ||| ||| ||| | | || | ||||| ||| |||| | | | | |||||||| | ||||||| || || |||| ||| ||||| ||||| |||||| | || || ||||| |||||||| |||||||||||||||| |||
cgtaaaaaagctgcttataactgtattgttgtcagtgcatcaattacgttaccgttttcctacttctgaacttataatttttcgttgttacggccattagGATGTGGCGGGAAATCAAACTCCTAGCTGAAAGAAAGCCAGTGATTGCATCAATGGCCGACGTAGCAGCTAGTGGAGGCTACTACATGGCAATGGCAGCC--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagttcgcttgtttaagtataaagtttttttgtcatgatcttctggatgtggagAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCAGGAGTTATT
tcttctg CT-rich tract
ttgtttaagtataaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatctttgtcatgaaattatgatgctaagtgcaagtattttgttgagttcgcttgtttaagtataaagtttttttgtcatgatcttctggatgtggagAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCAGGAGTTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - -catgaaa
- - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - -tgcaagt
- - - - - - - - - - - - - - - - - - - - - tgttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - gcttgtt