Sequence
atgc intronic sequence ATGC exonic sequence...gcccgagattgaccatgcacaagattgaccagccaacttctgatcctgattgcgctaaagcccaattgaaatcatatggtgttctctggtctttatccagCTGATGGATCTGATTTTGAAGCTCTAAATCATGCAATAGAGAGGCTGACATGCAATGATGCCAGTGTCTCTATTACTAAAGAAACTAGCACTGCTCTAGG
Basic information
species | Glycine max |
transcript | GLYMA18G46900.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46900.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g05250.3 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------------------gcccgagattgaccatgcacaagattgaccagccaacttctgatcctgattgcgctaaagcccaattgaaatcatatggtgttctctggtctttatccagCTGATGGATCTGATTTTGAAGCTCTAAATCATGCAATAGAGAGGCTGACATGCAATGATGCCAGTGTCTCTATTACTAAAGAAACTAGCACTGCTCTAGG
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gtatggcatctcctaccctcctgaaatagttttgtcattctattagttttaactagtctgattcagcctgataaaacactgcagttggtacataaaaaaagtctaatgctttgttgctttagttttttttt-tatgttgtc-actatatagagaat-atcctttcagGTTTCAAGCCTGCTAGA---CACATGGTCTTCTCTGGTCTATACCCAGCTGATGGCTCTGACTTTGACGCTCTTAGCCATGCAATTGAAAAACTAACATGTAA---------------------------------------------
upper sequence: GLYMA18G46900.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G39900.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------gcccgagattgaccatgcacaagattgaccagccaacttctgatcctga---ttgcgctaaagcccaattgaaatcatatggtgttctctggtctttatccagCTGATGGATCTGATTTTGAAGCTCTAAATCATGCAATAGAGAGGCTGACATGCAATGATGCCAGTGTCTCTATTACTAAAGAAACTAGCACTGCTCTAGG
| | || | | | | ||| | | | | || | || | | | | || | | ||||||||||| || || ||||||| ||||||||||||||||| ||||| || |||||| || |||| |||||||||||
gtatttattttttgtgtcttgtgcaactccag--taagcttcttaaagctcgctgacttgagtttaacttgtggaacctagGTTTCAAGCCGGT--GAGGCATATGGTGTTTTCAGGCGTTTATCCTGCTGATGGATCTGATTTCGAAGCACTTGGTCATGCCATGGAGAAACTGACATGCAA---------------------------------------------
upper sequence: GLYMA18G46900.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0108g00130.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------gcccgagattgaccatgcacaagattgaccagccaacttctgatcctg-attgcgctaaag--cccaa---ttgaaatcatatggtgttctctggtctttatccagCTGATGGATCTGATTTTGAAGCTCTAAATCATGCAATAGAGAGGCTGACATGCAATGATGCCAGTGTCTCTATTACTAAAGAAACTAGCACTGCTCTAGG
| | ||| | | | | | | | ||| || |||| ||| | ||| || ||||| || |||||||||||||| |||||||| ||||| |||||||| || || ||||||||||| ||||||||||||||
ttgcatttaacagtaacatattttttatgtcaaggatgtacacagtatttcctggtcctgataccttttattttgtgtgcacttctgtataatataaaagGTTTCAAACCTGCAAAACACATGGTATTTTCTGGTCTTTATCCGGCTGATGGCTCTGACTTTGAAGCACTTAACCATGCAATAGAAAGGCTGACATGCAA--------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgattgcgctaaagcccaattgaaatcatatggtgttctctggtctttatccagCTGATGGATCTGATTTTGAAGCTCTAAATCATGCAATAGAGAGGCTGACATGCAATGATGCCAGTGTCTCTATTACTAAAGAAACTAGCACTGCTCTAGG
cgctaaa putative branch site (score: 3)
tctttatcc putative PPT
aattgaaatcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcccgagattgaccatgcacaagattgaccagccaacttctgatcctgattgcgctaaagcccaattgaaatcatatggtgttctctggtctttatccagCTGATGGATCTGATTTTGAAGCTCTAAATCATGCAATAGAGAGGCTGACATGCAATGATGCCAGTGTCTCTATTACTAAAGAAACTAGCACTGCTCTAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - -catgcac
- - - - - - - - - - - - - - ccagcca
- - - - - - - - - - - - - - - - - - - -ctgatcc
- - - - - - - - - - - - - - - - - - - - - - - tgattgc