Sequence
atgc intronic sequence ATGC exonic sequencegtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
Basic information
species | Glycine max |
transcript | GLYMA20G24790.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcattt-gtctgttac-atatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
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-------------------------------ggagcaaatagtgcatgattgagccagttgggacatttac-----tatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattacc-------agATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatat--ttacatgtgtgattgtgttgtagagtctcctgaatgtactttac-tcctttaatatgcaattgt----aatcttggaa-cagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
| |||| ||||||| | | | | ||| | | | |||| | ||| |||| || ||| | | || ||| | |||| | |||| |||||||| || || | ||||| || ||||| |||||||||||||| ||| |||||||||| |||||||||| |||||||| ||||| ||||||||
----------------------------------------------ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtca---aatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatatttacatgt-gtgattgtgttgtagagtctcctgaatgtactttactcctttaatat-gcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
|| | | | | | | | ||| ||| | || || || | | || | | | || || || | | | | || || ||||||||||||| || | ||||||||||| || || |||||||||||||| || |||||||||||||||||||||| || || || || || || |||||
-----------------------------------ctaatcattattgaatcattgagttagtgtttgcatatagtcatacacttttgggacatcattagggc----tatgtctaaaacgtcgtggtctttatttt----cagATCAAGATTCAGTGCGTTTGTTGGCTGTTGAAGGTTGTGCTGCTCTTGGTAAATTGTTGGAGCCACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGT
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
| || | | | ||||| | | | | || | | | | | | | | || | | | | | | | | | || || ||||||||||||| || | |||||||||| || ||||||||||| ||||| || ||||||| ||||||||||| || ||||| || || || || |||||
---------------------------catgattgaa---tttgaatcattgggttagtgtttgcatatagtcatacgcatttgggacatcattaggactatgtctaaacctgctggtct-------ttatttt----cagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------gtaattgaatacatatttcttgttctttgtag-atggaaagtgtctgtcatttgtctgttacatat-ttacatgtgtgattgtgttgtagagtctcct------gaatgt--actttactcct-ttaatatgc----aattgtaatcttggaa-cagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
| || | | | || | | | || |||| || | |||||| | | | | | | || | | | ||| | | | ||| ||||| |||| | | |||| || | ||| ||| |||| ||||||||||| ||| | |||||||| || || ||||| |||||||| ||| ||||||| || || ||||||||||||| || | || ||||||||
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaat-taataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
|||| | | ||| || || | | ||| | | || || || || | || | | | | | |||||||||||||||| ||||| ||||| || ||||| |||||||||||||| || |||||||||| || |||||||| ||| || || || || |||||
-------------------------------------------------------------gtattga-acac-tgagcgt-ttatttactctacagcatatatatttgtcgaatttcatcttacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
|| || | || | | |||||| | | | || |||| || | | || | | | || || | ||| |||| || | | ||||||||||||| || ||||| |||||||| ||||| |||||||||||||| || |||||||||| || || ||||||||||| || || || || |||||
--------------------------ctgaagttaagcagaatta--cggttgtctacatctcagcttca-gtgtctttttatattataatattacagat-----------tttaagtatcttattgacat-tgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGTMapped 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|6501968|gb|AW203341.1|AW203341EST: TCATTTGAAGGCTGATGTCATGTCAATTTTTGACGATCTTACTCAAGATG ATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCA
genomic: TCATTTGAAGGCTGATGTCATGTCAATTTTTGACGATCTTACTCAAGATGgtaattgaat ... cttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCA
EST:
gi|15203829|gb|BI426597.1|BI426597EST: TCATTTGAAGGCTGATGTCATGTCAATTTTTGACGATCTTACTCAAGATG ATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCA
genomic: TCATTTGAAGGCTGATGTCATGTCAATTTTTGACGATCTTACTCAAGATGgtaattgaat ... cttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
ctttaat putative branch site (score: 4)
tttaatatgcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG