Sequence
atgc intronic sequence ATGC exonic sequence...acttttggggtattcatgaattaaaaattaaaattgctattacttttgataaatgctttcaatagctaaatagtggtcacttaccctcctcttgatgcagATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCATTGGTTAGTGACATACCAACCATAATTTTTGGAGCAGATGTAACCCACC
Basic information
species | Glycine max |
transcript | GLYMA20G28970.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 13
------acttttggggtattcatgaattaaaaattaaaattgctat-tacttttgata-aatgctttcaatagctaaatag------tggtcacttaccctcc----tcttgatgcagATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCATTGGTTAGTGACATACCAACCATAATTTTTGGAGCAGATGTAACCCACC
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gtaccaaatacttataaaccaagcagttaatacttagcttgtctacacaaatgtagtgtaatgcagtaagcagacttgcagcattgctaatgccttgcatttcggagttgtgatacagATGGGAGGAAGAAACACCGTGCTGCTGGATGCAATAAGTTGGAGGATTCCTTTGGTCAGTGACATACCAACTATTATATTTGGTGCAGATGTCACGCATC
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 14
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 12
-------acttttggggtattcatgaattaaaaattaaaattgctattacttttgataaatgctttcaatagctaaatagtggtcacttaccctcctcttgatgcagATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCATTGGTTAGTGACATACCAACCATAATTTTTGGAGCAGATGTAACCCACC
| | || ||| ||| || || | | | || || | | || | | | | ||| ||| ||| || | | | | | || ||||||||||| ||||||||||| || || || || |||| || || || || ||||| |||||||| ||||| || || ||||| ||||||||||| ||||
gtacttaccaccttggttatacatcaaatacagttcagaacagcaact--ttataagaga-------aatggctcgatattgactaatgatac--catcaaattcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCTTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACACC
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 13
-------acttttggggtattcatgaattaaaaattaaaattgctattacttttgataaatgctttcaatagctaaatagtggtcacttaccctcctcttgatgcagATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCATTGGTTAGTGACATACCAACCATAATTTTTGGAGCAGATGTAACCCACC
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gtacttaccaccttgtttatacataaaatacagtttagaacatcaactat-----ataagtggctctatta-ttgactaatggt-accaataa-------aattcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGGATTCCGTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACATC
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 11
acttttggggtattcatgaattaaaaattaaaattgctattacttttgataaatgctttcaatagctaaatagtggtcac--ttaccctcctcttgatgcagATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCATTGGTTAGTGACATACCAACCATAATTTTTGGAGCAGATGTAACCCACC
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-tagtctgtttattctttc-ttaccatctgaagtgtcaaattaaaatatttcaaagcatgaataattacagaatccttacgttttttcttttcatgatgtagATGGGTGGTAGAAACACTGTCCTTTTGGATGCTATCAGTTGCAGGATACCATTAGTTAGTGACATACCAACCATAATATTTGGAGCAGATGTGACGCATCMapped 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|7283776|gb|AW596379.1|AW596379EST: AAATCACTAAACAGTACCTGGCTAATGTGTCTCTGAAGATCAATGTGAAG ATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCA
genomic: AAATCACTAAACAGTACCTGGCTAATGTGTCTCTGAAGATCAATGTGAAGgtttgtttgc ... cttgatgcagATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCA
EST:
gi|19347375|gb|BM892255.1|BM892255EST: TGAAGATCAATGTGAAG ATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCA
genomic: TGAAGATCAATGTGAAGgtttgtttgc ... cttgatgcagATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgataaatgctttcaatagctaaatagtggtcacttaccctcctcttgatgcagATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCATTGGTTAGTGACATACCAACCATAATTTTTGGAGCAGATGTAACCCACC
tcacttaccctcctct CT-rich tract
tttcaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttttggggtattcatgaattaaaaattaaaattgctattacttttgataaatgctttcaatagctaaatagtggtcacttaccctcctcttgatgcagATGGGAGGTAGAAACACTGTACTTCTTGATGCTGTAAGCTGCAGAATACCATTGGTTAGTGACATACCAACCATAATTTTTGGAGCAGATGTAACCCACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- -tttgggg
- - - - - - - catgaat
- - - - - - - - - - - - aaattaaa
- - - - - - - - - - - - - - - - - tgctatt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttc