Sequence
atgc intronic sequence ATGC exonic sequence...tatgttcctaggctgtgttgggttcacttttaatttgtattatctcttgtagagttgtagttatgttgagatctgattgaattcacttttacttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGTAGCCGT
Basic information
species | Glycine max |
transcript | GLYMA07G03820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
--------tatgttcctaggctgtgttgggttcacttttaatttgtattatctcttgtagagttgtagttatgttgagat-ctgattgaattcacttttacttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGT-AGCCGT
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aaagctactatcatcatagaa-gtactatgtcatcatttagaaaatactatgacc-----agatgta--tgagctaatgtatttaccaagttttttaccaactt-tcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA-
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------tatgttcctaggctgtgttgggt--tcacttttaatttgtattatctcttgt-----agagttgtagttatgttgagatctgattga---attcacttttacttaat--cagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGT-AGCCGT
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gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataagcatgaatgtatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA-
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 1
--------------------------------------------------tatgttcctaggctgtgttgggttcacttttaatttgtattat-ctcttgtagagttgtagttatgttgagat-ctgattgaattcac------ttttacttaa--tcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGT-AGCCGT
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gtatgtggagttaattttcctagatgttgctcgtgtctacaagtcaatgaaaaattcctcaa-tattttgcactataagcaagaatgtatcattctgctagacaacagaaaatgtacctatatgtttaatgtatttatccattttctttcttaatatcagTGCCTCCGGCGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGATGATGGCCAGCCA-
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 4
tatgttcctaggctgtgttgggttcacttttaatttgtattatctcttgtagagttgtagttatgt--tgagatctgattg-aattcacttttacttaat-cagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGTAGCCGT
||| || | | | | | || | || ||| | | ||| |||| | || ||||| |||||| ||||||||||| || ||||||||||| || ||||| |||||||| || ||||| || ||||||| || ||||||||||||||||| ||
-----------------------------gtaaattttcctgacgatactgagatttcgatactgaaatgaaaagtatttgtaattggtggaggtgtgatgcagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGC
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 4
tatgttcctaggctgtgttgggttcacttttaatttgtattatctcttgtagagt----tgtagttatgttgagatctgattgaattcacttttacttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGTAGCCGT
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aatgttgt--ggttgaga-aaatgtgaacttattgtaagatacttttggtagtttctcttatattggtgttaaactcaaatatgaataacatc-gtttgtccagGGCTTCAGGGGAGCATGAATCTTCCAGACGGGTGAAGTCTGAACTTCTGGTTCAGGTTGATGGTGTAAACAACAGTTCTACAGGTGAAGATGGTAGTCGAMapped 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|11274568|gb|BF324910.1|BF324910EST: CCAAGCACAATATTCATTGATGAAATTGATTCTCTATGCAATTCTAGGGG GGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGT
genomic: CCAAGCACAATATTCATTGATGAAATTGATTCTCTATGCAATTCTAGGGGgtaagccttc ... acttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGT
EST:
gi|151402734|gb|EV272547.1|EV272547EST: CCAAGCACAATATTCATTGATGAAATTGATTCTCTATGCAATTCTAGGGG GGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGT
genomic: CCAAGCACAATATTCATTGATGAAATTGATTCTCTATGCAATTCTAGGGGgtaagccttc ... acttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtagagttgtagttatgttgagatctgattgaattcacttttacttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGTAGCCGT
atctgat putative branch site (score: 4)
cttttactt putative PPT
ttttacttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgttcctaggctgtgttgggttcacttttaatttgtattatctcttgtagagttgtagttatgttgagatctgattgaattcacttttacttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGTAGCCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - taggctg
- - - - - - - -tgttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg