Sequence
atgc intronic sequence ATGC exonic sequencegtagattatttataagcaattcctatgtttcatggctccttgtaagttgcttctcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
Basic information
species | Glycine max |
transcript | GLYMA06G15350.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 5
gtagattatttataagcaattcctatgtttcatggctccttgtaagttgcttctcttacctgtatgtatgattatgctcttctt----ttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
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gtaggtt--ctatggtcaattt-tatttgtgaaaattactc------taataccataatctccaggaattctcataccctcctaaaaatcagGTGCATTTGCTGTGTACTTGGAGCCTTGGCATGCGGATATTTTTGAGTTCCTTGATCTGAGAAAGAATCATGGGAAG
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 5
gtagat--tatttataagcaattcctatgtttcatggctccttgtaagttgcttctcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
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gtaaataccatcagttagttagacatggacctaat--ttacatgttcagtgttcaggatttct-tatggat--tcctaacattaatttagGTGCATTTGCTATATACTTGGAGCCTTGGCATGCTGATATTTTTGAGTTCCTTGATTTAAGAAAGAACCATGGAAAG
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 5
gtagattatttataagcaattcctatgtttcatggct-ccttgtaagttgcttctcttacctgtatgtatgattatgctcttct-----tttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
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----------------------gtatgtttcttcattatcgtcgcttttagttccttcatcttcagaaattctaacgagcttctaaaaacttagGTGCATTTGCTGTATACTTGGAGCCTTGGCATGCTGATATTTTTGAGTTCCTTGATCTGAGAAAGAACCATGGGAAG
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 5
gtagattatttataagcaattcctatgtttcatggctccttgtaagttgcttctcttacctgtatgtatgattatgctcttct----tttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
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-----------------gtatgctttttttcattatttccactt--ttagtaacatcgtcttcagaaattcttatgagcttctaaaacttagGTGCATTTGCTGTATACTTGGAGCCTTGGCATGCTGATATTTTCGAGTTCCTTGATCTAAGAAAGAACCATGGGAAG
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 5
gta-gattatttataagcaattcctatgtttcatggctccttgtaag---ttgcttctcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
||| || ||| | || | | | | || | || ||| || | |||| | |||| || |||| | | |||||| |||||||||||||||||||||||||||||||| || ||||| || | ||| | |||||||| ||||| |||
gtacaatcattaaaccttgctttattttgctgagggtaatgttcaaaaatttgattgtgccttgtgtaaatgtgataat-ctctgcatacagGTGCTTTTGCTGTGTACTTGGAGCCATGGCATGCTGACATATTTGAGTTTCTAGATCTTAGGAAAAACCATGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctccttgtaagttgcttctcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
ctcttac putative branch site (score: 3)
ttatgctcttctttt putative PPT
tatgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagattatttataagcaattcctatgtttcatggctccttgtaagttgcttctcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA