Sequence
atgc intronic sequence ATGC exonic sequence...atttgtgtaattttacaaaatctcataagtggttagtgtaatttacttttaatttatttatggtagttgttaattcatgtattctgaacatcttggacagGACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCTTCATGACATTGATGCATTATCAAAGATGGTTGATCCTTCTCTAAAAGGA
Basic information
species | Glycine max |
transcript | GLYMA13G37580.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G37580.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os02g07960.2 (Oryza sativa), 3'ss of exon 15
-----------------atttgtgtaattttacaa-aatctcataagtg-gttagtgtaatttacttttaat-ttatttatggtagtt-gttaattcatgtattctgaac-atcttggacagGACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCTTCATGACATTGATGCATTATCAAAGATGGTTGATCCTTCTCTAAAAGGA
|| || | || | | | |||||| || ||||| |||| || ||| || | | | | ||| | |||| | | | ||| | || ||||| | || || ||| || || |||||| | |||| ||||||||||||| | ||||||||||||||||||||||| | |||||
gtcagtgattcaccgtaatatgcatttcttaattttagtttcataattgtgttagatcaattgtctccaaatgttgtctgaactttctagtttgcttgcttattttccgttacaatatgcagTTCTCGTCCTCGTGCTGAACAACATCTTGTTAGATGGGCTGATTCTCAATTTCATGACATTGAGTCCATATCAAAGATGGTTGATCCTTCTATTCAAGGA
upper sequence: GLYMA13G37580.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G335638_T01 (Zea mays), 3'ss of exon 15
-------atttgtgtaattttacaaaatctcataagtggttagtgtaatttacttttaatttatttatggtagttgttaattcatgtattctgaacatcttgga-----cagGACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCTTCATGACATTGATGCATTATCAAAGATGGTTGATCCTTCTCTAAAAGGA
|| | | | | || | | ||| | | || |||| | || | | | | || || ||| | | || ||||| ||| | || || || | || || ||| || | ||||||| | |||||||||||||||| || | | ||||||||||||||||||||| | ||||
gtcagagatccattgcaatatgcatg-ttgaacaagagccttttgcaatt-atttgaatcacttctctcctaaaaattcatttttagtacttctttatgttggaatatgcagTTCTCGTCCACGTGATGAACAACATCTTGTTCGATGGGCTAATTCTCAGCTTCATGACATGGAGTCCCTGTCAAAGATGGTTGATCCTTCTATCCGAGGA
upper sequence: GLYMA13G37580.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G03390.1 (Arabidopsis thaliana), 3'ss of exon 15
atttgtgtaattttacaaaatctcataagtggttagtgtaatttacttttaatttatttatggt-agttgttaattcatgtattctgaacatcttggacagGACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCTTCATGACATTGATGCATTATCAAAGATGGTTGATCCTTCTCTAAAAGGA
||| || | || || | | | | ||| ||| | || |||||| | | | | | ||| || | |||| |||||||| ||||||||||||| || || ||||||||||| || |||||||| || ||||||||||| ||||| || |||
------------------gtatgcatgtcacattgttttatttgcttagttttctgtttccggttaagcatttattcatatcaacgagtcgatt---atagGGACCGGAGTAGAGGAGAGCAGTTCTTGGTGAGGTGGGCAATCCCACAGCTTCATGATATCGATGCATTGGGCAAAATGGTTGATCCATCTCTTAATGGA
upper sequence: GLYMA13G37580.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G20850.1 (Arabidopsis thaliana), 3'ss of exon 13
atttgtgtaattttacaaaatctcataagtggttagtgtaatttacttttaatttatttatggt--agttgttaattcatgtattc---tgaacatcttggacagGACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCTTCATGACATTGATGCATTATCAAAGATGGTTGATCCTTCTCTAAAAGGA
| ||||| | || | | || || ||||| |||| || ||| | | || | | || ||||| ||| | |||| ||||| ||||||||||| ||||| || || |||||||| ||||||||||||||| | |||||||| || || || || || ||
------------------------gtgagtgga-aatgaggtcttattcatatgtatttgtggtttgaacttttgttcttaaaaagaaatggaaacgttatgcagGAAACGGGATAGAGGAGAGCAATTTCTGGTGAGATGGGCAATCCCACAGCTTCACGACATTGATGCATTAGCGAAGATGGTCGACCCATCCCTCAAGGGT
upper sequence: GLYMA13G37580.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv12s0059g01920.t01 (Vitis vinifera), 3'ss of exon 14
atttgtgtaattttacaaaatctcataagtggttagtgtaatttacttttaatttatttatggtagttgttaattcatgtattct-gaacatcttggacagGACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCTTCATGACATTGATGCATTATCAAAGATGGTTGATCCTTCTCTAAAAGGA
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------gtgaatagaccaaattttatccaaattgggtttg--tgattatgtacccattt-tgctggct--tgatctttaccttcttaaataacatgtgcagCAAACGCAACCGAGGAGAAAAATTGCTGGTGAGATGGGCCATCCATCAGCTTCATGACATTGATGCTTTGTCAAGGATGGTTGATCCTTCATTGAATGGAMapped 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|15815431|gb|BI787706.1|BI787706EST: TTTGGAGTAGTTATGTTAGAACTTTTGACAGGCCGTCAGTCCTACGACAG GACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCT
genomic: TTTGGAGTAGTTATGTTAGAACTTTTGACAGGCCGTCAGTCCTACGACAGgtgagatcca ... tcttggacagGACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCT
EST:
gi|207813926|gb|GD785819.1|GD785819EST: TTTGGAGTAGTTATGTTAGAACTTTTGACAGGCCGTCAGTCCTACGACAG GACACGCCCTCGAGGGGAGCAGTTT
genomic: TTTGGAGTAGTTATGTTAGAACTTTTGACAGGCCGTCAGTCCTACGACAGgtgagatcca ... tcttggacagGACACGCCCTCGAGGGGAGCAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttaatttatttatggtagttgttaattcatgtattctgaacatcttggacagGACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCTTCATGACATTGATGCATTATCAAAGATGGTTGATCCTTCTCTAAAAGGA
tgttaat putative branch site (score: 3)
aatttatttatggta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgtgtaattttacaaaatctcataagtggttagtgtaatttacttttaatttatttatggtagttgttaattcatgtattctgaacatcttggacagGACACGCCCTCGAGGGGAGCAGTTTCTGGTGAGGTGGGCTATTCCTCAGCTTCATGACATTGATGCATTATCAAAGATGGTTGATCCTTCTCTAAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-tttgtgt
- - - - - - - -caaaatc
- - - - - - - - - - - - - - - -gttagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgaac