Sequence
atgc intronic sequence ATGC exonic sequence...tgttcttatagacaactgttacagctcatctttctcttctctttcttcctttcacttttcataagtttgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
Basic information
species | Glycine max |
transcript | GLYMA03G34340.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
tgttcttatagacaactgttacagctcatctttctcttctctttcttcctttcacttttcataagtttgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
| || | || || || || | | ||| | |||| || | || | | | | || | | | ||| ||||||||||| ||| ||||||||||||||||||| ||||| ||||| || || |||||||| | | || ||||| |||||||||| || || |||||
taccttttttcttttctttttattcttatttctagcttatagttctcttctttctgtcacacacctaaaatggccattgttcttattttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------tgttcttatagacaactgttacagctcatctttctcttctctttcttccttt------cacttttcataagtttgttagatataaccttctagagac------------ctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
||||| | ||| || | | | ||||| | || | | || | || ||| ||| | || | | | | ||| | | || || ||| || |||||||||||| ||||||||||||||||||| || || ||||| ||||| |||||||| | |||| ||| |||||||||| || || || |||||
gtccgcatttcttaaaaaaatatggtcttatccactgcaaattgagtgacatttagattgtacagaattttgttcattgggacctcttgttgacatattctttttgttgtttctcctggcttaaaatatactattctttctgttcctggctcaatactttaaaacacaatattgatccacttttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGTGGAAATTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 3
tgttcttatagaca-actgttacagctcatctttctcttctctttcttcctttcacttttcataagtttgttagatataaccttctagagacc---tgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
|||| | |||| | | || | | || | | | | | | | | || ||| | | || || ||| || | | | ||| || |||||||||||| ||||||||||||||||||| || || ||||| ||||| || |||||| | |||| ||| |||||||||| || || || |||||
---tcttgttgacatattcttgttgtttctcctgacttaatttataatgttctttctgttc-cagactcgtactttaaaacacagtatcaatccaatcttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGCGGAAACTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 2
-----tgttcttatagacaactgttacagctcatctttctcttctctttcttcctttcacttttcataagtttgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
| | | | | || || || || | || | | || ||||| || || | ||| || | | |||| | ||||||||||| ||| |||||||||||||||| || ||||| ||| | ||||||||||||| || | || ||||| ||||||||||| || || |||||
aacgacgagaatgttaccttgttttgcacctgattggtgcctctacctgtactgctttgtatttcagaatttaataaga----actacttgtgtatctgt-gtagAAATTTGAGGGAGATGTTCAAGATTGATGCAGCGGATTATATGGTTTCCATTTGTGGAAGTGACGCACTTAGGGAGCTATCTTCTCCTGGAAAGAGTGGA
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
tgttcttatagacaactgt-tacagctcatctttctcttctc--tttcttcctttcacttttcataagtttgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
| | ||| ||| || | ||| |||| | | || | | | | | ||| | |||| | | | |||| || ||||| |||| ||| |||||||||| ||||| || ||||| |||||||||||||||||||| |||||| | || ||||| |||||||| ||||| || ||
-------gttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattcattgctaaacct--tgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
tgttcttatagac-aactgttacagctcatctttctcttctctttcttcctttcacttttcataagtttgttagatataaccttctagagacctg-ttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
||| | || || || ||| || || | | | || | | | | || | ||| | | | | | | || || ||| ||| || ||||| || ||| |||| ||||||||||| || || ||||||||||||||||| ||||| ||| ||||||||||||| |||||||| ||||||||||||
tgtcttgatttaccaaaatttataga--attaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ34272 (Selaginella moellendorffii), 3'ss of exon 2
tgttcttatagacaactgttacagctcatcttt-ctcttctctttcttcctttcacttttcataagtt--tgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
|| | | ||| |||||| || | ||| | |||||| || | | || | || | | | ||| | | |||||||| ||||| || |||||||| ||||| ||| | || |||||||||||||| |||| | ||||| ||||||||||| || |||||
-----------------gtcctacttttccttagctcttccgatttcccatttggcatttcatcttttgacgctctgtacagtttttttt-gttgcatgtcagGCACCTTAGAGAGCTTTTCAAAATCGATGCTGCTGATTATATGCTCTCTCTTTGTGGAAACGATGCTCTTCGAGAACTTTCTTCTCCGGGCAAGAGTGGC
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 2
tgttcttatagacaactgttacagctcatctttctcttctctttcttcctttcacttttcataagtttgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
| ||| || | | || ||| | || | ||||| ||| | ||| | | || | | | ||| ||| | | |||||||| ||||| || |||||||| ||||| ||| | || |||||||||||||| |||| | ||||| ||||||||||| || |||||
---------gtcctacttttccttagctctttcgatttcccatttggcatttcatcttttgacgctctgtacagttt----tttttgttgcatgt--cagGCACCTTAGAGAGCTTTTCAAAATCGATGCTGCTGATTATATGCTCTCTCTTTGTGGAAACGATGCTCTTCGAGAACTTTCTTCTCCGGGCAAGAGTGGCMapped 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|254328419|gb|GR835384.1|GR835384EST: CATCAATCAGATGATTTTAAATGGAAAGATTATTGTCCCATGGTGTTTAG AAATTTGAGAGAGCTGTTCA-GAT-GATGCTGCCGATTAC
genomic: CATCAATCAGATGATTTTAAATGGAAAGATTATTGTCCCATGGTGTTTAGgttagtagta ... cctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctttcacttttcataagtttgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
atataac putative branch site (score: 3)
tttgttagatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttcttatagacaactgttacagctcatctttctcttctctttcttcctttcacttttcataagtttgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT
- - - - - - caactgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttcta