Sequence
atgc intronic sequence ATGC exonic sequencegtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
Basic information
species | Glycine max |
transcript | GLYMA03G40720.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 2
---------gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttatt-ttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
|| |||| ||| | | | | |||| || | | || ||| | || ||||| |||| || | | | || | || | | ||||| || |||||||| ||||| || || || ||||||||||||||| | || || || || || ||||||| |||||||||||||||||||||
gtccggctctctcttttttttttacatatttttactgttatatctcagctta--gcctgagcttgt-tttat-------ccatatcaattcatttgttacaactaatggtcctacagGTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAG
upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 2
-------------------gtca-ttcattttgaacaaacatgtgttattatgtcactttcaat-tgcatgatatagtctttatgtcgccgtcatag---tgatccttgttttttggt-ttatttttttt----agGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
| || |||||||| || || | || | ||| | |||| | | || | ||| || || | || | | || | ||||| | ||||| || |||||||| ||||| || || || ||||| ||||||||| | || ||||||||||| |||||||| |||||||||||||||||||||
gtatatatacaaatatattgccacttcattttctttctggctggtgaataacttcccaagtaatctagctgatgctatttgactgaagttttcaaagaacctattcatgcataatagtatcattttggtctggcagGTTCTTCTATGCCTCGAGTGCATGCATTTACCCTGAGTTCAAGCAGCTTGACACAAATGTGAGCTTGAAGGAATCTGATGCCTGGCCTGCTGAG
upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAA---ATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
| | | || || | | || | ||| || || | | || | | ||| | | ||||| |||| ||| ||||| |||||||| || ||||||||||||||||| || || |||||||||||||| | ||||||| ||||||||||| ||||| |||||||| |||
-------------gttagttagattttgttttcttcggttt--tcgcagtttacggtttcttaaaacaagttaaaaagat--tggattttttgtttgcttt----agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S171_56V6.2 (Physcomitrella patens), 3'ss of exon 1
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgcc--gtcatagtgatccttgttttttggtt-tattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGT---TTGAAGGAGTCTGATGCCTGGCCTGCTGAG
||| | | | || | | | | | || || | || || | | | | || | | | | | || |||||||| ||||| || || || |||||||||||||||||||| ||| ||||||| | ||||| |||||||||| || || ||||| ||| |
----------gtgagtacaatcttcttcctttaccgatcgtagagagattgctcccgtttcaaatcttttggttttgtcggttcctgagtggagttggtggatgttgcagGTTTTTCTATGCTTCAAGCGCGTGTATCTATCCTGAATTCAAACAGCTGGAGACTGACGTGAGCAGCCTGAAGGAGTCGGACGCTTGGCCCGCTCTG
upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
|| | | | | | || || | | || | | ||| |||| || || ||||||||||| || ||||| || || || || || || |||||| ||||||| || ||||||||||||||||| ||||| ||||| || |||
--------------------------------gtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttgg-------cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgc-cgtcatagtgatc-----cttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
| || || || || | || || | | || | ||| || | | | | || || || ||||||||||| || ||||| || || || || || || |||||| ||||||| || ||||||||||||||||| ||||| ||||| || ||
------------------------------------------gtagcctgtgat-gtttctaagttgttcttcccaaggatttggagctcactctctcgcttggcttcc--agATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA
upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10353 (Selaginella moellendorffii), 3'ss of exon 1
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgc-cgtcatagtgatccttgttttttggtttatttt---ttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
| || || || || | || || | | || | ||| | | | | || || || ||||||||||| || ||||| || || || || || || |||||| ||||||| || ||||||||||||||||| ||||| ||||| || |||
------------------------------------------gtagcctgtgat-gtttctaagttgttcttcccaaggatttggagctcactctctctcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
|| | | || | | || || | | || | | ||| |||| || || ||||||||||| || ||||| || || || || || || |||||| ||||||| || ||||||||||||||||| ||||| ||||| || |||
--------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttgg-------cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAGMapped 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|213616469|gb|DB965530.1|DB965530EST: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATCAATGGTGTTAAGAG GNNNNNNNATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATCAATGGTGTTAAGAGgtcattcatt ... ttttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
tttatttttttt CT-rich tract
ttgttttttggtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG