Sequence
atgc intronic sequence ATGC exonic sequence...caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
Basic information
species | Glycine max |
transcript | GLYMA16G26940.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 2
caaattgaattttag--ctcataactgttt-agtatgcttttagtgatttttctgtt-tataaggtt----taagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
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--------ctcttagtatttaagactatctgaaaacacttccaaaataaagtatattgtgtacggttgcagcaagtacttgcaatgactagtctttcatattattcagGTTGATCCTGATGAGGTCAATGCGTTGGCACAACTAATGACATGGAAGACGGCCGTGGCTAATATTCCATATGGAGGAGCTAAAGGTGGAATAGGATGCA
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG----------------------------------------------------
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------------------------------------gttggtgaaaaatctggtcctgatgtttgaaatcctttg-acaacc---------------caggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 3
caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgag----tagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
|| | || | || | | ||| | | | |||| | || | ||| || || | | | || | | |||| ||||||| || |||||||| ||||| ||||||||| | ||||| ||||| ||||| ||||| || ||||||||||| || |||||||| ||||| || |||
---atccatttccttcaaattaat-tttcctcttcatttaagactcattgaaatccgttggtgaaaaatctggtcctgatgtttgaaatcctttgacaacccagGTTGATCCTGATGAAGTTAATGCCTTGGCACAATTGATGACTTGGAAAACAGCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTA
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
| ||||| | | ||| | | | || | || | | ||| || | || ||| | | |||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || || || ||||| ||||| || |||||||||||||| || ||||
----gtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattggcatgaagtaaac-------cagatttcggtaatcg-----acagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 4
--------caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
|| | |||| | | | || | | |||| | ||| || | | |||| |||| | || || |||| ||||||||| |||||||| || ||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| ||||| ||||||||||| ||||| |||
ccagggttttcatgtagctttaaattaaatctactctcca-gcttgggaacagatttgtgctattgcagtttcagttt----ggatgatcgcata---gcttttgtagGTTGACCCAGATGAGGTAAATGCTTTGGCACAACTAATGACGTGGAAGACAGCAGTAGCAAATATTCCATACGGTGGGGCCAAAGGAGGGATAGGATGTA
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 2
caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
|| | | | | | ||| | ||| | ||| | || ||| | |||||||| ||||| |||||||||||| |||| || || ||||| ||||| || || |||||||| | ||||| |||||||| || |||||||| || |||
------------------gtagacaggaaagagaaaccaaagaacgctcttgt-------gattataattgctcttttatttttgttct--------tagGTTGATCCAGACGAAGTGAATGCTCTGGCCCAGCTCATGACTTGGAAAACCGCGGTAGCAAAGCTTCCATACGGTGGTGCAAAGGGAGGAATCGGCTGTA
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 2
caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
||| | | | | | || | | || | ||| | || ||| | |||||||| ||||| |||||||||||| |||| || || ||||| ||||| || || |||||||| | ||||| |||||||| || |||||||| || |||
------------------gtaaacaggaaagagaaaccaaagaacgctcgctcttgtga---ttgtaattgctcttttatttttgttct--------tagGTTGATCCAGACGAAGTGAATGCTCTGGCCCAGCTCATGACTTGGAAAACCGCGGTAGCAAAGCTTCCATACGGTGGTGCAAAGGGAGGAATCGGCTGTAMapped 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|254319541|gb|GR829053.1|GR829053EST: ATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCAGATACCATCCTGAG GTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACA
genomic: ATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCAGATACCATCCTGAGgttagttata ... gcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACA
EST:
gi|23731633|gb|BU763952.1|BU763952EST: ATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCAGATACCATCCTGAG GTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACA
genomic: ATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCAGATACCATCCTGAGgttagttata ... gcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
ccctcac putative branch site (score: 3)
tttataaggtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - -gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccctc