Sequence
atgc intronic sequence ATGC exonic sequence...cttacattagcaattctatttctggagatacattgtagtcaactacactttttaaattctgcgtgaggctaaatgcatgttgtggttgaatcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA
Basic information
species | Glycine max |
transcript | GLYMA05G33420.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 1
cttacattagcaattctatttctggagatacattgtagtcaacta--cactttt-taaattctgcgtgaggc-taaatgcatgttgtggttgaatcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA
||| |||| || | || |||| | ||| | || || || |||| | || | | | | | | | | | | |||||| |||||||||||||| | ||||| ||||||| || |||||||||||||||||||||| | ||||| || ||||| |||| || | |||||
-ttatatta-taacttcatgactggt--tttcttggaatctgcttatcagttttatgaagatagtactatgtgcttctactcaaccaagatcattgacctgcagGAAGTGCTGGTGATGTGCTAGAAGACAATCCAGTTGGGCGGTTGAAGGTTTTTGTTTATGACTTGCCAAGCAAGTATAACAAGAGGATAGTCGCCAAGGA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 1
---------cttacattagcaattctatttctggagatacattgtagtcaactacactttttaaattctgcgtgaggctaaatgcatgttgtggttgaatcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA
|| | ||| ||| | ||| || | || | | | || || || | | | | || |||||| ||| ||| |||||| |||||||||||||| ||||||||||| || || || ||| | ||||| | ||| ||||| || ||||| || || || ||||| | ||| | |||||
gctatgcttctaaaatttagaatattcttttccctaattctgtgcaa--------ggtctatagatactccatagcttttgcttaatattgtggc-gaaacaaatgcagGAAGTGCTGGTGATGTGTTGGAAGATGACCCTGTTGGGAGGCTTAAGGTCTATGTCTATGATCTCCCAAGCAAGTACAACAAGAAGCTGCTGAAGAAGGA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G023020_T01 (Zea mays), 3'ss of exon 1
cttacattagcaattctatttctggagatacattgtagtcaactacactttttaaattctgcgtgaggctaaatgcatgttgtggttg-aatca----attgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA
| | || ||| | || | | ||| ||| || |||| | || ||| ||| || || | ||| | | || ||| |||||||||||||| || |||||| |||| ||||| ||||||||||| || ||||||| | ||||| || || || ||||| || | |||||
---atgtagaaaaatctccatatgattgttttgctttgtctacttcatattttgt-tcatgtgtgttgcttg-tgtggactgaaacagcaattatgaaactgtagGGAGTGCTGGTGATGTGTTAGAAGATAATCCTGTGGGTAGGTTGAAGGTCTTCATTTATGACTTACCAAGGAAGTACAACAAGAAGATGGTCACCAAGGA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
---cttacattagcaattctatttctggagatacattgtagtcaactacactttttaaattctgcgtgaggctaaatgcatgttgtggttgaatcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA
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agcattatctttcaggttctgtgattg-agctacatagt--taatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 1
cttacattagcaattctatttctggagatacattgta----gtcaactacactttttaaattctgcgtgaggctaaatgcatgttgtggttgaatcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA
| | ||| ||| | | | | | | || ||||||| |||| ||||| | |||| | ||| ||||| | | || |||||| |||||||| || |||||||| ||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||| ||||||||||||||
tgtcctttaaaaatctgctagcagcaaaattttcctaacctgtcaactgaacttaaaaaatta---ggatctctaaccacgccttg-ggttgcacctcatgtagGTAGCGCTGGTGACGTCTTGGAAGACAATCCAGTGGGAAGGTTGAAAGTTTTTGTTTATGAACTTCCAAGTAAATACAACAAGAAGATTCTGCAAAAGGA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 1
-cttacatt--agcaattctatttctggagatacattgtagtcaactacactttttaaattctgcgtgaggctaaatgcatgttgtggttgaatcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA
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cccgagagttaaacaattctaagttctcttgagcagtttgatttaatggggactctgaag--catgtaatctgatctccactttgggtttcaatgaat-gcagGAAGTGCTGGTGATGTTTTGGAAGATGATCCAGTAGGAAGGTTGAAGGTTTTTGTGTACGAGCTTCCAAGCAAATACAACAAAAAGATCCTTCAGAAGGAMapped 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|4293421|gb|AI442045.1|AI442045EST: AGTTGGAGCTGTGGAGCTGGGCAGGAACCAACCCACTGAAAGAATTTCAG GTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTT
genomic: AGTTGGAGCTGTGGAGCTGGGCAGGAACCAACCCACTGAAAGAATTTCAGgtgctttttg ... tcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactttttaaattctgcgtgaggctaaatgcatgttgtggttgaatcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA
ggctaaa putative branch site (score: 3)
tttaaattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttacattagcaattctatttctggagatacattgtagtcaactacactttttaaattctgcgtgaggctaaatgcatgttgtggttgaatcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg