Sequence
atgc intronic sequence ATGC exonic sequence...cagcatattcaacaaaagttctacgaatctgatgaaatagttaccatttcagtggattattttctagttattagtttgtatcttggcacacatttgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT
Basic information
species | Glycine max |
transcript | GLYMA05G28400.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G837351_T01 (Zea mays), 3'ss of exon 3
-cagcatattcaacaaaagttctacgaatctgatgaaatagttaccatttcagtggattattttctagttattagtttgtatcttggcacacatttg--ttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT
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gctgcatatgtatggcaaattgcttga-catgtgaaaacag--acagattcactatgctgatctcagtatcttgattaattattaagcctttgctacatttagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCACCACAAGACTATGATCAGTTCATCATGGGGAGCCCCTGCAGCG
upper sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G058930_T01 (Zea mays), 3'ss of exon 6
-----cagcatattcaacaaaagttctacga-atctgatgaaatagttaccatttcagtggattattttctagttattagtttgtatcttggcacacatttgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT
| |||||| | || || || || ||| || | | | || || | | | | ||| | || ||| ||| || ||||| || || || |||||||| | ||||| ||||||||||||||||| || | ||||||||||||| || ||||||||||| || ||||| ||
aatagctgcatatgtatggcaaattgcttgacatgtgaagacagattcactatgctgatct-cagtatcttgattaattattaagcctttgctacatgc-----agTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCTATAAGACTATGATCAGTTCATCATGGGGAGCCCCTGCAGCG
upper sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------cagcatattcaacaaaagttctacgaatctgatgaaatagttaccatttcag---tggattattttctagttattagtttgtatcttggcacacatttgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT
|| | ||| | | || | | | | | | | | | | ||| || | | | || ||| | | ||| |||||||||||| ||| ||||||| | | ||||||||| |||||||||||||| | ||||||||| ||||| || | |||||||| || || || ||
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaaacctaatatctcgcttaggttattttgagtaacagctatttatatgt-cttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG
upper sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G14030.1 (Arabidopsis thaliana), 3'ss of exon 3
cagcatattcaacaaaagttctacgaatctgatgaaatagttaccatttcagtggattattttctagttattagtt-tgtatc-ttggcacacatt-tgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT
| || | || | || | ||| ||| | || | | ||||||| | |||| ||| ||| | | |||||||||||||| || || ||||| | | ||||||||| || ||||||||||| | ||| ||||| ||||| ||| |||| ||||| || ||| ||
---------------gtatcttattg-caaaacaaagcattttctgttttagtt-----tcttgtcgctattagtcatatatcattgttggttattgtatcagGTGGGAGAAACCAGGACATAGTCCTTTGTATGGGTATGATTTTTGGTACCAACCTCGGCACAAGACCATGATCAGCACATCTTGGGGAGCACCTAAAGCC
upper sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 3
cagcatattcaacaaaagttctacgaatctgatgaaatagttaccatttcagtggattattttctagttattagtttgtatcttggcacacatttgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT
| ||| | || || | | | | || |||| | | | | | | || || | | | ||| | | || | | || ||||||||||| ||||| ||||| || ||||| || || |||||||||||||| | || ||||| ||||| || ||||||||||| || ||||| |||
gaacatgtccagggaatggttttagtataacatgagccaacctctgacattgagcacagtattttaagtttgattttccactccttttgatatatatcagATGGGAGAAACCAGGGCATAGTCCGTCTTTTGGCTACGATTTCTGGTACCAACCCCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCTMapped 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|7145625|gb|AW507547.1|AW507547EST: TGGATTTCTTCTCCTTGATCATGAATTTAATTTGAAAGGAAG GTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCA
genomic: TGGATTTCTTCTCCTTGATCATGAATTTAATTTGAAAGGAAGgtaccctttt ... catttgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcagtggattattttctagttattagtttgtatcttggcacacatttgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT
attattttctagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagcatattcaacaaaagttctacgaatctgatgaaatagttaccatttcagtggattattttctagttattagtttgtatcttggcacacatttgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - aacaaaa
- - - - - - - - - - - - - -tctgatg
- - - - - - - - - - - - - - - - - - - - - -ccatttc