Sequence
atgc intronic sequence ATGC exonic sequence...atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
Basic information
species | Glycine max |
transcript | GLYMA03G39500.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
|||| | | | | | | | | ||| | | | | | || | ||| || | | || | | | |||| | |||| || || ||||||| |||||| | |||||||||||||| || |||||||| | ||||||||||| || || |||||||||||||||||||
atctttgagctcctctgaaaagtttcttagtgctacatgatttgcctttttttttatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
atctatactattgttcta--cttgcgttaga-tgtttgcatacatgtctatgtgctgcatcagcatttgga-atggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
| | ||||| | | | | ||| | | ||| | | | | | | | || | || | | ||| |||| | ||| | | |||||||| || || || || ||||| ||||||| |||||||||||||| ||||| ||||| || || ||||| || ||||| ||||||||||| |||||||
--gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatg-tctatgc-gaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
---atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
| | || | | | ||| || | | | ||| | | | ||| | | | ||| | | ||||||||||| || || |||||||| ||||||| |||||| || ||||| || |||||||| |||| || ||||||||||| ||||| || ||||| ||||
agacattgcattaccatggaaaatatgttttattctgatgt---tatcttgagcacactttatattttcaagtatgatagtaacgatgttcttgctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G173849_T01 (Zea mays), 3'ss of exon 1
---atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
|| | || | | | | | | || | || ||| | | | | | |||| | | | | | ||| | | ||||||||||| || || |||||||| ||||||| |||||| || ||||| || |||||||| |||| || ||||||||||| ||||| || ||||| || |
cgacaaaatggagatattgcattaccatggaaaatctgttt-tat-tctgagca-tactttatattttgaagtagggtagtaacgatgttcttgctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATCG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaatttt--acagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
|| | | | | || || || | ||| |||| | | | || ||| | ||| | | | || | | ||||||| || ||||| |||||||||||||||| ||||| || | ||| ||||||||||| || || || |||||||| |||||||| ||||| ||||| |
----gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatattttttgaacca-aacggaa-agtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------------------------------------atctatac-tattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttgg----aatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
||| | || || || | | | | ||||||| | | ||| | | ||| |||| || | || || | |||||||||| || |||||||||||||| ||||||| ||||||||||| || || |||||||| |||| |||||||| || ||||||||||| ||||| ||||
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtg-acgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 5
atctatactattgttctacttgcgttagatgtttgcat-acatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattt-tacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
| | | ||| | || ||||| | | | ||| || || | ||| | || | ||| || ||| | | |||||||| || || || || || |||||||||| |||||||||||||| || |||||||| ||||| ||||| || |||||||||||||||||||| || |
aattctctagttgccatgtagcaatt--atgttagtgtgatgtgtgcattctttgatctattcttttattaaatgtaaccaaacaacttggaatgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 5
atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
| | ||| || | || | | || | || || ||| | |||||||| || ||||| |||||||| || || ||||||||||||||||||||||||||| | || ||||| || || || |||||| | || || ||||
------------------------------------gttc-tgtgtaggaactctttacctgtcgggttcttaaactcaagct--tctggttcgtcgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 5
atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaatt--ttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
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-----------------------------------------gttctgtgtaggaactctttacctgtcgggttgttaaactcaagcttcttgttcgttgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTGMapped 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|209718166|gb|BW657812.1|BW657812EST: CACAAACAAATGCCACTTTTCTGAAGTTGGCAGGTCCACAGCTGGTCCAG ATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCA
genomic: CACAAACAAATGCCACTTTTCTGAAGTTGGCAGGTCCACAGCTGGTCCAGgtatgactct ... aattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCA
EST:
gi|16281884|gb|BI944719.1|BI944719EST: CACAAACAAATGCCACTTTTCTGAAGTTGGCAGGTCCACAGCTGGTCCAG ATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAACTGGCA
genomic: CACAAACAAATGCCACTTTTCTGAAGTTGGCAGGTCCACAGCTGGTCCAGgtatgactct ... aattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
atctaac putative branch site (score: 2)
aataatctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - tacttgc
- - - - - - - - - - - - - - - - - gcataca
- - - - - - - - - - - - - - - - - - - - - - - - gtgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacctga