Sequence
atgc intronic sequence ATGC exonic sequence...ctgcaaagtgaaatcttgataatggggcatataagaatgtgtccacaatatgaaattattgtactatcattttgatgctttttttaaatctgttctgcagTTTATCCCATACTCATTTATAGAGAAAGAAGCAAGTCATGTTGAGGGTTTTAGTCCTGAGTTAGCACTAGTTACAATTGGGGGTGGAAAGGAACTTGAAG
Basic information
species | Glycine max |
transcript | GLYMA16G29890.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G29890.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 2
ctgcaaagtgaaatcttgataatggggcatataagaatgtgtccacaatatgaaattattgta-ctatcattttgatgctt----tttttaaatctgttctg-cagTTTATCCCATACTCATTTATAGAGAAAGAAGCAAGTCATGTTGAGGGTTTTAGTCCTGAGTTAGCACTAGTTACAATTGGGGGTGGAAAGGAACTTGAAG
| | | || | | || | || | || | ||||| | | | | || || | || | | | | ||| || | ||| || ||||| || |||||||||||||||||||| ||||| ||||||||||| || ||||| || ||| | ||| | || || ||||| || ||||| ||||| || |
---ctaggcgattgcctcatgctt---tatctgagttagagtccatagtttccatttgttatgtcttatgtgtaggttcttatgcttgtcccttctattgcatcagTTCATTCCATACTCATTTATAGAGAAGGAAGCTAGTCATGTTGAAGGGTTTAGCCCGGAGCTTGCATTGGTCACCATTGGAGGAGGAAAAGAACTAGAGG
upper sequence: GLYMA16G29890.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 2
--ctgcaaagtgaaatcttgataatggggcatataagaatgtgtccacaatatgaaattattgtactatcattt-tgatgctttttttaaatctgttctgcagTTTATCCCATACTCATTTATAGAGAAAGAAGCAAGTCATGTTGAGGGTTTTAGTCCTGAGTTAGCACTAGTTACAATTGGGGGTGGAAAGGAACTTGAAG
|| | | || ||| | | || | || | | | || | | | | |||| | || | ||| ||| || |||||||||| |||||||| ||||| ||||||||||| || |||||||| ||||||||||| |||| || ||||| |||| || ||||| |||||||| |
ttaatcataatccaaatttgtttgttggtgaaattc-atcttctttcttatgctcttatgtcacattgggatttatagtgatggttt--ggtcttttgtgcagTTTATACCATACTCGTTTATTGAGAAAGAAGCTTCACACGTTGAGGGATTTAGTCCTGAACTAGCTCTTGTTACTGTTGGAGGAGGAAAAGAACTTGAGG
upper sequence: GLYMA16G29890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 2
ctgcaaagtgaaatcttgataatggggcatataagaatgtgtccacaatatgaaattattgtactatcattttgatgctttttttaaatctgttctgcagTTTATCCCATACTCATTTATAGAGAAAGAAGCAAGTCATGTTGAGGGTTTTAGTCCTGAGTTAGCACTAGTTACAATTGGGGGTGGAAAGGAACTTGAAG
|| | | || | | || | || | | | | ||| | | | | | ||| |||| | | | |||||||||| |||||||||||||| || ||||||||||| |||||||| ||||| ||||| || |||||||| || |||||||| || ||||||||||||||||
ttggcagttaaattaccagtgataagcatgctacagaaaggaagaaggtgtgataggcatttccagttgtttgatgtctttatcctgttttccattgcagTTTATACCATACTCATTTATTGAAAAAGAAGCAAGCCATGTTGAAGGTTTCAGTCCAGAATTAGCACTTGTGACAATTGGAGGGGGAAAGGAACTTGAAGMapped 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|20075374|gb|BQ094157.1|BQ094157EST: TGAATGTGAAGTTCAAGGAGACCGGACATAGTAACATGTATTTTCCGCAG TTTATCCCATACTCATTTATAGAGAAAGAAGCAAGTCATGTTGAGGGTTTT
genomic: TGAATGTGAAGTTCAAGGAGACCGGACATAGTAACATGTATTTTCCGCAGgtaaaagtta ... tgttctgcagTTTATCCCATACTCATTTATAGAGAAAGAAGCAAGTCATGTTGAGGGTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatatgaaattattgtactatcattttgatgctttttttaaatctgttctgcagTTTATCCCATACTCATTTATAGAGAAAGAAGCAAGTCATGTTGAGGGTTTTAGTCCTGAGTTAGCACTAGTTACAATTGGGGGTGGAAAGGAACTTGAAG
ttttgat putative branch site (score: 4)
tctgttct putative PPT
aaattattgtactatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgcaaagtgaaatcttgataatggggcatataagaatgtgtccacaatatgaaattattgtactatcattttgatgctttttttaaatctgttctgcagTTTATCCCATACTCATTTATAGAGAAAGAAGCAAGTCATGTTGAGGGTTTTAGTCCTGAGTTAGCACTAGTTACAATTGGGGGTGGAAAGGAACTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
-tgcaaag
- - - - - - - - - - - - - gcatata
- - - - - - - - - - - - - - - - - - - -tgtccac