Sequence
atgc intronic sequence ATGC exonic sequence...ttggttattttttagacccactttatttgtctctctctgtatttgtgctttgaaatacactagaatagtttaaaatcttcagcattttaataattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
Basic information
species | Glycine max |
transcript | GLYMA16G05570.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 10
ttggttattttttagacccactttatttgtctctctctgtatttgtgctttgaaatacactagaatagtttaaaatcttcagcattttaataa--ttttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
| | | | ||| | || | || | ||| ||| || | ||| | || |||| | ||| | || || ||| |||||||||||||||||| | || ||||| ||| || |||||||| || | ||| | | |||||||||||||||||| |||||||||| ||||||||||
----------gtgatatatagtttgta-aactttttccgggtttctgcattcttg-aaacttgt-tattttagaggctttaatgaacaaacaaaatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
upper sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G41120.1 (Arabidopsis thaliana), 3'ss of exon 10
ttggttattttttagacccactttatttgtctctctctgtatttgtgctttgaaatacactagaatagtttaaaatcttcagcattttaataattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
| || | | | | || |||| | ||| | | || | | |||| | ||||||| ||| ||||||||||||||||||||||| ||||| |||| || |||||||||||||| ||| | | ||||||||| ||||| | |||||||| | ||||||||||
-----------gtgattatgtattttccatattttccttcattt-taatttttgaggctttata----tctaaagac----acatttta-taa----cagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
upper sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G26820.1 (Arabidopsis thaliana), 3'ss of exon 12
--ttggttattttttagacccactt---tatttgtctctctctgtatttgtgctttgaaatacactagaatagtttaaaatcttcagcattttaataattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
| ||||| || | | || | | || | || || | | ||| ||| ||| | | | | | | | | || |||||||||||||||||| | || ||||| ||||||| |||||||| || | ||| | | ||||||||| ||||| || ||||| |||| ||||||||||
gttatgttataattaatatattgttgcgtggtgacctttttcggtttctacaattttggata--ttagtgttttggaggttaacatgtaaagagagacttcacagGGTGAAGAATACAAGCTGTTTTGGCCAGAACAATCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCGAAAATCGTTCCTTTCGGTGTTGTTGGAGAAG
upper sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0068g01430.t01 (Vitis vinifera), 3'ss of exon 10
ttggttattttt-tagacccactttatttgtctctctctgtatttgtgctttgaaatacactagaatag--tttaaaatcttcagcattttaataattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
||| | | | | || || | | | | ||| | | || |||| ||| ||| ||| | || ||| | || ||||||| ||||||||||| || ||||| |||||||||||||||| | || || || || ||||||||||||||| |||| ||||| | ||||||||||
-aaaatatgtgtgcatgtatatttcata-gccatgaagtagacatgtcggggtcacaattttaaaataccttttgcaatactcaat-tgttcatattgtttagGGTGAGGAATACAAGTTGTTTTGGCCAGAACAATCTGAGTTTGTCCGAATTGCGGCTAGGTTTGGAGCCAAAATTATACCCTTTGGAGTTGTTGGAGAAG
upper sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------------------------------------------------------------------ttggttattttttagacccactttatttgtctctct--ctgt-----atttgtgctttgaaat-----acactagaatagttt--aaaatcttcagcattttaataattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
|| | | | | | |||| ||| | | |||| | | ||| || ||| | || | | ||| || || | | || | | | | |||||||| ||||||||||| || ||||| || |||||||||| | | ||||| || ||||||||||||||||||||||| ||||| | ||||||||||
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagtattaaactcttttttgcaacacccaac-tgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAGMapped 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|15812273|gb|BI784548.1|BI784548EST: CTCATGTCCTATTGTATCCAGGAGGGATGCGTGAGGCTCTTCATAGGAAG GGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATG
genomic: CTCATGTCCTATTGTATCCAGGAGGGATGCGTGAGGCTCTTCATAGGAAGgtaaatccca ... taattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttgaaatacactagaatagtttaaaatcttcagcattttaataattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
ttttaat putative branch site (score: 3)
ttttc putative PPT
aatagtttaaaatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggttattttttagacccactttatttgtctctctctgtatttgtgctttgaaatacactagaatagtttaaaatcttcagcattttaataattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - gacccac
- - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - -gaaatac