Sequence
atgc intronic sequence ATGC exonic sequenceATTTATCATAGTTCCATTCATGGAGTTATTGTTGCCAGTATTCCTTAAATTATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttattgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtag
Basic information
species | Glycine max |
transcript | GLYMA18G48050.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G48050.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g39550.3 (Oryza sativa), 5'ss of exon 3
ATTTATCATAGTTCCATTCATGGAGTTATTGTTGCCAGTATTCCTTAAATTATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttattgta----ctcatcaaacaatacatgct----tgactactggtgt----gctttattatcactcaattttgggaaggcttaacttgtag---
|| ||||| ||||||||||||||||| || | ||||| ||||| || |||||||| || ||||| || || |||||||| ||||||||||||||| |||| || | | |||| || ||| | ||||| ||| | | ||| || || | ||| | || | | | |||| || ||
GTTCATCATTGTTCCATTCATGGAGTTCTTACTTCCAGTGTTCCTCAAGTTATTTCCAAATATGCTTCCCTCAACTTTCCAAGACAAGATGAAAGAAGAGgt-atgtcagtgtaacaacttgagttacataatatgctaatgtgatcaatattgtttaggcgtttgattttctctacttggtgttgtctta-ctgatacttt
upper sequence: GLYMA18G48050.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G160801_T01 (Zea mays), 5'ss of exon 2
ATTTATCATAGTTCCATTCATGGAGTTATTGTTGCCAGTATTCCTTAAATTATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttattgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtag--
||||| || ||||||||||||||| | ||| ||||||| ||||| || || || || |||||| |||| ||||||||||||||||| ||||||||| |||| || | | || || | | | | | | | || || |||| | | ||| ||
TTTTATTATCGTTCCATTCATGGAGCTCTTGCTGCCAGTGTTCCTCAAGTTGTTCCCAAACATGTTGCCATCCACTTTCCAGGACAAAATGAAAGAAGAGgt--ttgacctagaacaattaatctgtcttgtcaatagaattactaaatgctaacatggctcatactgcattcgtcttgctccatacag
upper sequence: GLYMA18G48050.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G145905_T02 (Zea mays), 5'ss of exon 3
ATTTATCATAGTTCCATTCATGGAGTTATTGTTGCCAGTATTCCTTAAATTATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGg--tgattttattgtactcatcaaacaatacatgcttgactactggtgtgcttta-ttatcactcaattttgggaaggcttaacttgtag-----------
|| ||||| |||||||||||||| || || ||||||| ||||| || |||||||| |||||||| || || |||||||||||||| ||||| ||| ||| || | || || | | | || || | | || || ||| || || || | | ||| |
GTTCATCATTGTTCCATTCATGGAATTCTTACTGCCAGTCTTCCTCAAGTTATTTCCAAACATGCTTCCATCAACTTTCCAGGACAAAATGAAGGAAGAGgtatggtcttgac-tatttgtaagttgcaactacctgaaattatgttgcttattagttgccatgtgtccctgcaagtggaatactaccatatgcataagtc
upper sequence: GLYMA18G48050.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G314656_T01 (Zea mays), 5'ss of exon 3
ATTTATCATAGTTCCATTCATGGAGTTATTGTTGCCAGTATTCCTTAAATTATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttattgtactcatcaaacaatacatgcttg-actactggtgtgctttattatcactcaattttgggaaggcttaacttgtag----------------
|| ||| | ||||| ||||||||||| || ||||||| ||||| || |||||||| |||||||| || || |||||||| ||||| ||||||||| |||| | | || | | | || || | || | | | || | | || ||| | | | | || ||||
GTTCATCGTTGTTCCTTTCATGGAGTTCTTACTGCCAGTGTTCCTGAAGTTATTTCCAAACATGCTTCCATCAACTTTCCAAGACAAAATGAAAGAAGAGgta--tgtgtttgattggtttaagaacctgagattatattggtctgatggtgttacatttctcggcatgtgaatag--tactctgtatgccacaaactcactgc
upper sequence: GLYMA18G48050.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G65540.1 (Arabidopsis thaliana), 5'ss of exon 2
ATTTATCATAGTTCCATTCATGGAGTTATTGTTGCCAGTATTCCTTAAATTATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttattgtactcatcaaacaa----tacatgcttgactactggtgtgcttt-attatcactcaattttgggaaggcttaacttgtag-------------------------------------------------------------------------
|| || || ||||||||||||||||| ||| | || || || ||||| || || || ||||||||||| || ||||||||||| |||||||||||| |||| | ||| || || | | || | | | | | | ||| ||| | || | ||||||| | || | ||
TTTCATTATTGTTCCATTCATGGAGTTTTTGCTACCGGTGTTTCTTAAGTTGTTCCCAAACATGCTGCCGTCAACTTTCCAGGATAAGATGAAAGAAGAGgtactgttaaaaaacctattttattgcttctctattccttatacgtcatttatttttatttttacattgatctgggaagtatgaattggtttgatctttcattctcgcgctgtcactcttgcctgtttctcaagtatgaatctaaaattcacgtttattttgcag
upper sequence: GLYMA18G48050.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ23574 (Selaginella moellendorffii), 5'ss of exon 3
ATTTATCATAGTTCCATTCATGGAGTTATTGTTGCCAGTATTCCTTAAATTATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttattgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtag
|| ||||| || || || |||||||| | | || || || || ||| | |||||||||||||| || || || || || |||||||||||||||||||| | ||| | || | | || | | | | || | | || | |
GTTCATCATCGTCCCTTTTATGGAGTTCCTTCTCCCGGTGTTTCTCAAAGTCTTTCCCAACATGCTCCCATCGACGTTTCAAGACAAGATGAAAGAACAGgtaagcggtttgctaccttctaggatcacgtacaacgatctttgt-ttccttgctgtag----------------------------
upper sequence: GLYMA18G48050.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ11458 (Selaginella moellendorffii), 5'ss of exon 2
ATTTATCATAGTTCCATTCATGGAGTTATTGTTGCCAGTATTCCTTAAATTATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttattgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtag
|| ||||| || || || |||||||| | | || || || || ||| | ||||||||||||||||| || || || || |||||||||||||||||||| | | ||| | || | | || | | | | || | | || | |
GTTCATCATCGTCCCTTTTATGGAGTTCCTTCTCCCGGTGTTTCTCAAAGTCTTTCCCAACATGCTGCCATCGACGTTTCAAGACAAGATGAAAGAACAGgtaagctgtttgctaccttctaggatcacgtacaacgatctttgt-ttccttgctgtag----------------------------Mapped 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|14205472|gb|BG839150.1|BG839150EST: TATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAG GAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTT
genomic: TATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttat ... taacttgtagGAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTTATCATAGTTCCATTCATGGAGTTATTGTTGCCAGTATTCCTTAAATTATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttattgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC