Sequence
atgc intronic sequence ATGC exonic sequence...cacgttcagcacttcttattttcatgttttacatttttatgactgcttcagataaggggaagaataaagtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT
Basic information
species | Glycine max |
transcript | GLYMA04G00250.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g47530.1 (Oryza sativa), 3'ss of exon 5
------------------------cacgttcagcacttcttattttcatgttttacatttttatgactgcttcagataaggggaagaataaagtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT
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gtacttgtctttccaagaaccatacgagttatcaatgttttgtcctaataaagaagctgcttttccttgatgtttttgtgatattgtggata-tctgatagcatcgttctcccgccaa-cacagATGGGCATTGCTTCCATTGTTCACCTCTATGTGTTCCCTGCGAAGCCCTATGAGCTGCAAGCCAACCAGTCACCAGGAAACGTCTCAGTACTCGGGGATT
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G082181_T01 (Zea mays), 3'ss of exon 7
----------------cacgttcagcacttcttattttcatgttttacattt---ttatgactgcttcag-------ataaggggaagaataaa-gtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT
||| |||| ||||| || ||| | ||| | | | |||| || || | ||| | | | |||| || ||| || || |||||||||||||||||| | |||||||| |||||||| ||||| ||||| |||| | | | | | |||| | |||| || ||||| || |
gtattcatccttccagggtgtttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccaggacagATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGGGGACT
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G082181_T02 (Zea mays), 3'ss of exon 7
----------------cacgttcagcacttcttattttcatgttttacattt---ttatgactgcttca-------gataaggggaagaataaa-gtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT
||| |||| ||||| || ||| | ||| | | | |||| || || | ||| | | | |||| || ||| || || |||||||||||||||||| | |||||||| |||||||| ||||| ||||| |||| | | | | | |||| | |||| || |||||
gtattcatccttccagggtgtttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG-----
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------------------cacgttcagcacttcttattttcatgttttacatttttatgactgcttcagataaggggaa-gaataaagtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT
|||| |||| |||| || | | || | ||| || | || ||| || | | || |||| | || || |||||||| ||||||||| | |||||||||||||| || |||||||||||||||| | |||||||||||||||| ||||| ||||||||||||||| || |
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaaca-cttgtgctggtccagtgcagATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGGTGACT
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G38360.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------------------cacgttcagcacttcttattttcatgttttacatttttatgactgcttcagataaggggaa-gaataaagtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT
|||| |||| |||| || | | || | ||| || | || ||| || | | || |||| | || || |||||||| ||||||||| | |||||||||||||| || |||||||||||||||| | |||||||||||||||| ||||| |||||||||||||||
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaaca-cttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG-----
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g03670.t01 (Vitis vinifera), 3'ss of exon 7
cacgttcagcacttcttattttcatgttttacatttttatgactgcttcagataaggggaagaataaagtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT
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tgaactccttatcttatgcctatacgctgcaaaatttattggtaatgtcatcttcatacaaaactaaagtttaacaggttcatgtattcatccagcacagATGGGCATCGCTTCAATTGTTCACCTGTATGTATTCCCTGCCAAGCCTTATGAGCTAATGGGAGACCGGTTATCTGGAAGTGTTTCGGTTCTTGGAGACTMapped 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|21887467|gb|BQ740680.1|BQ740680EST: AAGGCTTGCAGTTCAAGTCAAGTGTCCGAGATTTCATCATTTGCATTGAG ATGGGCATTGCTTCCATAGTTCACCTGTATGTGATTCCAGCAAAGCCTTAT
genomic: AAGGCTTGCAGTTCAAGTCAAGTGTCCAAGATTTCATCATTTGCATTGAGgtagatgtcc ... tcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcagataaggggaagaataaagtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT
gtttaac putative branch site (score: 3)
aagaataaagtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacgttcagcacttcttattttcatgttttacatttttatgactgcttcagataaggggaagaataaagtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
cacgttc
- - - - gcacttc
- - - - - - - - - - -tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtattc