Sequence
atgc intronic sequence ATGC exonic sequence...aaaaggaggataaggttcctccaccttttcatatgattgatgttcataaagcctttatttttggtgatcctctgagattttccttttgtgattgtagcagCTTTATTCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA
Basic information
species | Glycine max |
transcript | GLYMA12G09430.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G09430.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g37170.8 (Oryza sativa), 3'ss of exon 1
------------aaaaggaggataaggttcctccaccttttcatatgattgatgttcataaagccttt-------------atttttggtgatcctctgagattttccttttgtgattgtagcagCTTTAT---TCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA---
|| | | | | || ||| | | | | || | | ||| | ||| | | | | ||| || | || || |||||| || | ||| ||||| | |||||||||||| ||||| |||||||||||||| | || ||
gtgtgatcccacaactcccctacatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggccttta-attccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
upper sequence: GLYMA12G09430.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g37170.3 (Oryza sativa), 3'ss of exon 2
aaaaggaggataaggttcctccaccttttcatatgattga----tgttcataaagcctttatttttggtgatcctctgagattttccttttgtgattgtagcagCTTTAT---TCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA---
| | | | | | || | | | || ||| | || | || ||| | | | | ||| || | || || |||||| || | ||| ||||| | |||||||||||| ||||| |||||||||||||| | || ||
acatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggccttta-attccatttgtatgtatgcagCAGCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
upper sequence: GLYMA12G09430.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g37170.5 (Oryza sativa), 3'ss of exon 3
aaaaggaggataaggttcctccaccttttcatatgattga----tgttcataaagcctttatttttggtgatcctctgagattttccttttgtgattgtagcagCTTTAT---TCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA---
| | | | || | | | || ||| | || | || ||| | | | | ||| || | || || |||||| || | ||| ||||| | |||||||||||| ||||| |||||||||||||| | || ||
---tcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggccttta-attccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
upper sequence: GLYMA12G09430.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 3
aaaaggaggataaggttcctccaccttttcatatgattgatgttcataaag----cctttatttttggtgatcctctgagattttccttttgtgattgtagcagCTTTATTCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA
| | |||| ||||||||| |||||| |||| |||| || | | | |||||||| |||| ||| |||||||| ||||||||||| | |||||||||||||||| ||||||| | || || |||||||||||||| ||||||||||||||||||||||||||| ||||
---aaggggattaggttcctctcccttttgatatt-ttgaaaatcttgggggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCAAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaagcctttatttttggtgatcctctgagattttccttttgtgattgtagcagCTTTATTCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA
tttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaggaggataaggttcctccaccttttcatatgattgatgttcataaagcctttatttttggtgatcctctgagattttccttttgtgattgtagcagCTTTATTCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA
- - - - - - - - - ctccacc
- - - - - - - - - - - - - - - - - - -tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - gccttta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctctg