Sequence
atgc intronic sequence ATGC exonic sequence...ctgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctacatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
Basic information
species | Glycine max |
transcript | GLYMA18G22780.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 2
ctgcatattatctatagcataaattccatgattt-tttcaatctcaccagcgatctacatatggtgacaatcagttaacttggttatttctg---gtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
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----acattggcaacagttacatctgcgcatttgacttgtagtttgctctcgtcttttaattctcaaatgtttgtcttctgagatttacctgtccatgttacagTTTACCATGCCCTAAAGGGCATCATTAAGGCGAAATATGGTCAAGATGCATGCAATGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 2
ctgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctacatatggtgacaatcagttaacttggttatttctggtag---aacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
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tttgttataaaagtaaacatctatatttgggatttttgcttcttctagctggtcacttcatctt--ctatcc-tcacttggaatatccttgttatggtaacagTTTACCATGTCCTGAAGGGCATCATTAAGGCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 2
ctgcatattatctat-agcataaattccatgattttttcaatctcaccagcgatc--tacatatggtgacaatcagttaacttggttat-ttctggtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
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-tatgttgtatcagtgaatagctatattgggactatttgcttctgctagctggtcacttcatcttctaacc-tcacttggaatatccttgttctggta--acagTTTACCATGTCCTGAAGAGCATCATTAAGTCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
-ctgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctacatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
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catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttc-tgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
upper sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
ctgcat-attatctatagcataaattccatgattttttcaatctcaccagcgatc-tacatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
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ttctatgattatgcagttctttagtt--gtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAGMapped 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|16105109|gb|BI892849.1|BI892849EST: ACCAGTTGGAGCAACTTCATTTGCTGAGGCTCTCCGCATGGGCAGTGAAG TTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCAT
genomic: ACCAGTTGGAGCAACTTCATTTGCTGAGGCTCTCCGCATGGGCAGTGAAGgttagaaacc ... ggtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagcgatctacatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
agttaac putative branch site (score: 3)
ttatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctacatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
-tgcatat
- - - - - - - - - - - - -ccatgat
- - - - - - - - - - - - - - - - - - - - -ctcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgac