Sequence
atgc intronic sequence ATGC exonic sequence...tgtcatgcacatattccatctgactcattgattaagctgcttatttccaattatctgcctctagttcatggtttgcaccaattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC
Basic information
species | Glycine max |
transcript | GLYMA20G33770.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g41370.1 (Oryza sativa), 3'ss of exon 1
tgtcatgcacatattccatctgactcattgattaagctgcttatttccaattatctgcctctagttcatggtttgcaccaat-------tctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC
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--atgagtgcatgctgtttctgg---ggagatttatataagaactgctagtcatat--ctagagaatacaattgacaacaatgtatggtttgctttaatttatgcagGTGGTGCAGTTGTTTTCATGTGTGGACAAGATAAGCTTTCTGGACTGGGCACCGGATTCAGAGTATATTCTATGTGGACTTTACAAGCGACCCATGGTGC
upper sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G07590.1 (Arabidopsis thaliana), 3'ss of exon 1
tgtcatgcacatattccatctgactcattgattaagctgcttatttccaattatctgcctctagttcatggtttgcaccaattctttttg-gcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC
|| | | | | | || | | | || | || | | | | | | | |||| | | | |||||||||||||| |||||||| |||||||| || || ||||| || |||||||| |||||||| || || |||||||| ||||| || ||||| |||||||| |
tgctaaat-tttggaacttttaaccttagagatgataaatgtcgttgaagtttttttttctttctatgtactaatcttcaatgttatggatgtgaatgcagGTTGTGCAATTGTTTTCTTGCTTAGATAAAATAAGCTACATAGAATGGGCTCTTGATTCAGAGTACATTCTTTGTGGTCTTTATAAAAAACCGATGATTC
upper sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 2
---tgtcatgcacatattccatctgactcattgattaagctgcttatttccaattatctgcctctagttcatggtttgcaccaattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC
|| | | ||| ||| | | | || |||| || ||| | || || || | ||| | || | || || || || |||||||||||||| || || ||||| || ||||| ||||| ||||| ||||| |||||||| ||||| || ||||| |||||||| || | || |||||||
ggatggtaaac-catgttcttttttgttttttttttaaagatttttttttttttaatttgttggtaaataatga--aacttaaaattttattttctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCTCTTGATTCAGAATACATACTTTGTGGTCTCTATAAGAGACCAATGATAC
upper sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S52_72V6.1 (Physcomitrella patens), 3'ss of exon 1
tgtcatgcacatattccatctgactcattgattaagctgcttatttccaatta--tctgcctctagttcatggtttgcaccaattctt---tttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC
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--tcatattcct--tgaatcgaaaatgggtatgaacttcagcatcagtgcttagatttggtttcttacaacaatttggatcacattttgggtctgggtt-tgcagGTTGTGCAGTTGTACTCTTGCTTGGACAAGATTAGCTATGTAGAATGGGCCCCAGATTCGGAGTATCTTCTATGTGGTCTCTTCAAGCGAGCTATTGTTCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|207684004|gb|GD667463.1|GD667463EST: GACCGTTTCTTTCAAG GTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCC
genomic: GACCGTTTCTTTCAAGgtttcgtttt ... gcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCC
EST:
gi|15814586|gb|BI786861.1|BI786861EST: CCGTTTCTTTCAAG GTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCC
genomic: CCGTTTCTTTCAAGgtttcgtttt ... gcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaattatctgcctctagttcatggtttgcaccaattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC
aattcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcatgcacatattccatctgactcattgattaagctgcttatttccaattatctgcctctagttcatggtttgcaccaattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC
- -catgcac
- - - - - - - - - -ctgactc
- - - - - - - - - - - - - - - - -aagctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcacca