Sequence
atgc intronic sequence ATGC exonic sequence...tcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
Basic information
species | Glycine max |
transcript | GLYMA09G28980.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G28980.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
-tcaactttcaagcaattttt-tgtgcaatttgagggattttgctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
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ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctct--acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
upper sequence: GLYMA09G28980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
tcaactttcaagcaattttttgtgcaatttgagggattttg--ctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
|||| | | | |||| | | | | || || ||||||||||| | ||||||| |||| | || | | ||||| |||| | | |||||||||||||||||||| || | ||||| |||||||| |||||||| |
tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctct--actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
upper sequence: GLYMA09G28980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G146786_T02 (Zea mays), 3'ss of exon 2
-------------------------------------tcaactttcaagcaattttttgtgcaatttgagggattttg--ctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
|||| | | | |||| | | | | || || ||||||||||| | ||||||| |||| | || | | ||||| |||| | | |||||||||||||||||||| || | ||||| |||||||| |||||||| |
tcacacgaggatgccttgcttttacttaaatgcttgatcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagGGATTTTGGTTCTCT--ACTCGGTGGTTGATACCAACAGATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
upper sequence: GLYMA09G28980.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 3'ss of exon 2
tcaactttcaagcaattttttgtgcaatttgagg-gattttgctgataacatgccccggcagggatattggcttc-ctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
| | | | | || | | | | || || ||| |||||||| |||||||||||||||| ||| | | ||| ||| | |||| ||||||||||||||||||| || || ||||| || ||||||||||||||||
gtgattcttatgt--ttgactctatattgggactcgacttttctgataacttgccccggcagggataacggccccgccacattttctggttattgcatatagATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
upper sequence: GLYMA09G28980.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------tcaactttcaagcaattttt-tgtgcaatt------tgagg---gattttgctgataacatgccccggcagggatattggcttc-ctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
| | ||| ||| || ||| | | || | || ||| |||||||| |||||||||||||||| ||| | | ||| ||| | |||| ||||||||||||||||||| || || ||||| || ||||||||||||||||
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
upper sequence: GLYMA09G28980.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 2
tcaactttcaagcaattttttgtg-caatttgagg-gattttgctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
| | || |||| | || || | || || || ||| |||||||||||||||||||||||| ||||| | || |||||| ||||| ||||||||||||||||||| ||||| || |||||||||||||||||||||||||
--acatctcttctctttttatatgacattctgtggagagttttctgataacatgccccggcagggatcttggcattgcctaccgggtggttgatgtgagcagATGCAAGAGGTTGCAGGGGAACGTGGAGGTTACCTTCATGGACGAGGCGMapped 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|120532700|gb|EH260833.1|EH260833EST: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG ATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
genomic: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAGgttagcgcat ... atgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
EST:
gi|120532341|gb|EH260474.1|EH260474EST: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG ATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
genomic: AAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAGgttagcgcat ... atgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
ggctgat putative branch site (score: 4)
atatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - ttcaagc
- - - - - - - - - tttgtgc
- - - - - - - - - - - - - - -tgaggga
- - - - - - - - - - - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - catgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtggc