Sequence
atgc intronic sequence ATGC exonic sequence...tgtgaagcctgccagtatgagtgattgacataattggattagctattgttgctgttaatgtgtaagtttcctaattatttacccaattttatttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAA
Basic information
species | Glycine max |
transcript | GLYMA07G01440.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
tgtgaagcctgccagtatgagtgattgacata-attggattagctattgttgct-gttaa-tgtgtaagtttcctaattatttacccaattttatttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAA
| || | | |||| || ||| | ||| ||| | | | | | ||||| || | | | || | ||||||||| ||||| ||||| ||||| |||||||| ||||| |||||||||||||||| ||| | ||||| || || ||| | || || | ||||| |
--tttagtgtcttgttcatttcacttgatatttgttgtgtcggcttgatttgttcgccagctaaatcagtttgtatcttgatcagtatgctacatgt-ttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 2
tgtgaagcctgccagtatgagtgattgacataattggattagctattgttgctgttaatgtgtaagtttcctaattattta-cccaattttatttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAA
| | ||||| | | || | | | | ||| ||| | || | | | ||||| | | || | | | |||||| || || || ||||| |||||||||||||| |||||||| |||||||| ||||| ||| || || || || ||| | ||||| ||||||||
ttccacacctgctctgctctttaataagtg-aggaatttcacttcgtgtgagtgtagaatgtcgccttgcatgttgatttaacactcttctttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 1
tgtgaagcctgccagtatgagtgattgacataattggattagctattgttgctgttaatgtgtaagtttcctaattattta---cccaat------tttatttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAA
| || | | | ||| || | || | || |||||||| ||| || || |||||| || || | ||| ||| || | |||| ||||| |||||||| ||||| ||||| || |||||||| || |||||||||||||||||||| || || || ||||| |||||| |||| ||||||||
-----actttgttgggaagtgtggtt----tttttagtgtatgtattgttggatgaaatctgcgagattcctattttctttgcttctaatgtggtgtttcattttgcagTTGATATTATTTCTGCAATTGAGTTTGATAAATCTGGTGACCACCTTGCTACTGGTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 1
tgtgaagcctgccagtatgagtgattgacataattggattagctattgttgctgttaatgtgtaagtttcc-taattatttacccaatttt--atttctt-cagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAA
|| | | || || | ||| | | | | | | || | | | | | | || || | || | ||| || |||| || || || || || || ||||| |||||| ||||||||||||| || ||||| ||||| || || |||||||| |||||||| | | ||| ||
---gagacgagaaggtgtggg-atttggtgtctaggagctggatgccaatagtggttttttcttcgagactgtagttgacacctgggttctggattggttgcagTTGACATTATATCCGCAATCGAATTCGACAAGACTGGTGATCATCTCGCAACTGGAGATCGCGGAGGGCGAGTAGTCCTCTTTGACAGAAGTGATGATAA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 1
tgtgaagcctgccagtatgagtgattgacataattggattagctattgttgctgttaatgtgtaagtttcc-taattatttacccaatttt--atttctt-cagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAA
|| | | | || || | ||| | | | | | | || | | | | | | || || | || | ||| || |||| || || || || || || ||||| |||||| ||||||||||||| || ||||| ||||| || || |||||||| |||||||| | ||| ||
---gagacgagacggtgtggg-atttggtgtctaggagctggatgccaatagtggttttttcttcgagactgtagttgacacctgggttctggattggttgcagTTGACATTATATCCGCAATCGAATTCGACAAGACTGGTGATCATCTCGCAACTGGAGATCGCGGAGGGCGAGTAGTCCTCTTTGACAGATGTGATGATAAMapped 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|33389971|gb|CA853178.1|CA853178EST: ATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAG TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
genomic: ATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttg ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
EST:
gi|207824963|gb|GD797179.1|GD797179EST: CGGCCGGGGAGGAAGTTCAGGAAG TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
genomic: CGGCGGGGGAGGAAGTTCAGGAAGgtaattgttg ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
EST:
gi|208259705|gb|GE059735.1|GE059735EST: CGGGGGAGGAAGTTCAGGAAG TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGGTCATCTTGCTA
genomic: CGGGGGAGGAAGTTCAGGAAGgtaattgttg ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgctgttaatgtgtaagtttcctaattatttacccaattttatttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAA
tcctaat putative branch site (score: 2)
ttttatttcttc putative PPT
taattatttacccaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgaagcctgccagtatgagtgattgacataattggattagctattgttgctgttaatgtgtaagtttcctaattatttacccaattttatttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - gcctgcc
- - - - - - - - -tgagtga
- - - - - - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacccaa