Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaatcaccttttaagctttacaatacattcagagccttgctgttggccattccaaattgaataaatcatgatgcagctgcagATGAAGATCCATTGCCGGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCTTTCCTGGAAGGGAACTTCAAGCATGTGGATACTCCATCAATGGCACTAC
Basic information
species | Glycine max |
transcript | GLYMA20G35770.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35770.3 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os05g01060.1 (Oryza sativa), 3'ss of exon 12
---gtaagtaatcacct-tttaagctttacaatacattc-----agagccttgctgttggccattccaaattgaataaatcatg---atgcagctgcagATGAAGATCCATTGCCGGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCTTTCCTGGAAGGGAACTTCAAGCATGTGGATACTCCATCAATGGCACTAC
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gtgttacatatttatatatattatatttattgaatattcttcttagtatttctttggctcttattgtaaaacatatttttcatgaataagcagCTGCAGATGATGACCCACTACCAGCCATAGAAGGGCTACGAATCACAGGTGAAGCTTTTCCTGGAAGAGAGCTTCAAGCAAGTGGCTACTCTATCAATGG------
upper sequence: GLYMA20G35770.3 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g01800.2 (Oryza sativa), 3'ss of exon 12
gtaagta--atcaccttttaagctttacaatacattcagagccttgctgttggccattccaaattgaataaatcatgatgcagctgcagATGAAGATCCATTGCCGGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCTTTCCTGGAAGGGAACTTCAAGCATGTGGATACTCCATCAATGGCACTAC
|||| || || | | || | || | | || | | ||| | | | | | || | ||| |||||| || || |||||| |||| | |||||||| |||| ||| |||| ||||| ||||||||||| ||||| |||||| | || ||||||| ||||||
gtaattactattagaaataaatttatatatttgtttaacactaatgcaatctgatgatatattcctcttttatgaatatgtagCTGCTGAGGATGATCCACTGCCAGGCATAGAGGGCCTTCGAATCACAGGTGAAGCTTTTCCTGGAAGAGAACTCCAAGCAAGCGGGTACTCCACCAATGG------
upper sequence: GLYMA20G35770.3 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G036206_T01 (Zea mays), 3'ss of exon 12
gtaagtaatcaccttttaagctttacaatacattcagagccttgctgttggccattccaaattgaataaatcatgatgcagctgcagATGAAGATCCATTGCCGGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCTTTCCTGGAAGGGAACTTCAAGCATGTGGATACTCCATCAATGGCACTAC
||||| | || || || | | || | || | | ||| || || || |||||||||| || ||||||||||| | ||||| || |||| ||| |||| ||| | ||||||||| |||||||||||| |||||||||||||||||||
----gtaattattattgaattaagttcgtattgtttaacactgcatattaatggatgcctatt--atgaac----atacagCTGCAGAGGATGATCCATTGCCAGGCATAGAAGGGCTTCGAATCACAGGTGAACCTTTTCCTGGACAAGAACTTCAAGCAGGTGGATACTCCATCAATGG------
upper sequence: GLYMA20G35770.3 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 11
gtaagtaat-caccttttaagctttaca-atacattcagagccttgctgttggccattccaaattgaataa--atcatgatgcagctgcagATGAAGATCCATTGCCGGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCTTTCCTGGAAGGGAACTTCAAGCATGTGGATACTCCATCAATGGCACTAC
|| || |||| || | | || || | | | | | || ||| || || | ||||| |||||| || ||||| | || || ||||| || || | ||| |||| ||||||||||||||||| |||||||||||| |||| ||||| ||| ||||
----gtgtcgcatctttaaatccgtgcatatgcctactatattatctcagttatgatggtaaacaacatttttatgaatgtgcagTTGCAGAGGATGATCCGCTTCCAGCCATAGAAGGACTGCGAATCACAGGTGAAGCCTTTCCTGGAAGAGAACTTCAAGCAAGTGGGTACTCTATCCATGG------Mapped 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|17963067|gb|BM269820.1|BM269820EST: TCCTTATTTACCACCAGTTCTTGAAGAACCTTCTTCTTCATTTTCTGAGG ATGAAGATCCATTGCCGGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCT
genomic: TCCTTATTTACCACCAGTTCTTGAAGAACCTTCTTCTTCATTTTCTGAGGgtaagtaatc ... gcagctgcagATGAAGATCCATTGCCGGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCT
EST:
gi|21888872|gb|BQ742085.1|BQ742085EST: TCCTTATTTACCACCAGTTCTTGAAGAACCTTCTTCTTCATTTTCTGAGGCTGCAG
genomic: TCCTTATTTACCACCAGTTCTTGAAGAACCTTCTTCTTCATTTTCTGA----G--Ggtaagtaatc ... gcagc
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagagccttgctgttggccattccaaattgaataaatcatgatgcagctgcagATGAAGATCCATTGCCGGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCTTTCCTGGAAGGGAACTTCAAGCATGTGGATACTCCATCAATGGCACTAC
aaattgaataaatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaatcaccttttaagctttacaatacattcagagccttgctgttggccattccaaattgaataaatcatgatgcagctgcagATGAAGATCCATTGCCGGCTATAGAGGGTCTTCAAATTTCAGGAGAAGCCTTTCCTGGAAGGGAACTTCAAGCATGTGGATACTCCATCAATGGCACTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG