Sequence
atgc intronic sequence ATGC exonic sequence...cttgaatacttgctgcactctctgttttgattcatgttgttgttattatttgtcattgataactgagcatttgtgcggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
Basic information
species | Glycine max |
transcript | GLYMA06G05580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------cttgaatacttgctgca-ctctctgttttgattcatgttgttgttattatttgtcat-tgataactgagcatttgtgcggatg-ttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
||| || | | | || || | | |||||| || |||| | | || || | || || | || ||| | | || | |||||| || ||||| ||||| ||||| ||||| || ||||| || || |||||||| |||||||| || ||||| ||||| ||||| ||||||||||| ||
gtatctatgcttacggtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 3
cttgaatacttgct-gcactctctgttttgattcatgttgttgttattatttgtcattgataact-------gagcatttgtgcggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
| || |||| | | ||| | | | || | ||| ||||| ||| || || || |||| | || | | || | ||||||||||||||| ||||| ||||| ||||| || || || || ||||| ||||| |||||||| ||||| || || || ||||| ||||| ||||| ||
---gtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 3
cttgaatacttgctgcactctctgttttgattcatgttgttgttattatttgtcattgataactgagcatttgtgcggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
|| || || | || | || || |||| ||| | |||| | ||| | || |||| | || | | || | ||||||||||||||| ||||| ||||| ||||| || || || || ||||| ||||| |||||||| ||||| || || || ||||| ||||| ||||| ||
-----gtatgtg-tgtaggaacttgaaaaagctatctt-ttgtgatt-tatgtcttagatta--gaacattatctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------cttgaatacttgctgcactctctgttttgattcatgttgttgttattatttgtcattgataac--tgagcatttgtgcggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
||| | | || | | ||| || | |||| | | | || | || || | | || ||| | ||| || | | |||||| |||||||| ||||| ||||| ||||| || ||| |||| ||||||||||| |||||||| || |||||||| ||||||||||||||||| || ||
gtaagtgaagtatttcctttgagaacacattctatacataccttcattgtttctgtctagttttgtattttcttttgtttgtttcaaagcttagtactgttactcttaaacaacctcatattggttttgttatttatcattagGTTTCGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATTATTCCATTCTGCAAGGGTCTTGATGTGATCCAGCAAGCTCAATCTGGAACTGGAAAGACCGC
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.1 (Arabidopsis thaliana), 3'ss of exon 3
------cttgaatacttgctgca-ctctctgttttgattcatgttgttgttattatttgtcat-tgataactgagcatttgtgcggatg-ttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
||| || | | | || || | | |||||| || |||| | | || || | || || | || ||| | | || | |||||| || ||||| ||||| ||||| ||||| || ||||| || || |||||||| |||||||| || ||||| ||||| ||||| ||||||||||| ||
gtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g01000.t01 (Vitis vinifera), 3'ss of exon 2
-----cttgaatacttgctgcactctctgttttgattcatgttgttgttattatttgtcattgataactgagcatttgtgcggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
| | ||| ||| | | | || | ||| ||||| | | | |||| || || ||| | || | | | || |||| | ||||||||||||||||||||||||||| ||||| || |||||||| ||| ||||||||||||||| |||||||||||||| ||||||||||||||||| ||
tgcatcataaatcactgcc-tgatttttattgttatttatgttttga--gccacct-tcatggaaaaatgaaaagctgaaagttggatctaac-tttcttggtagGTTTTGAGAAGCCCTCTGCAATTCAGCAAAGAGGTATTGTTCCCTTCATCAAGGGGCTTGATGTAATTCAGCAAGCACAGTCTGGAACTGGAAAAACAGC
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S136_29V6.4 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------cttgaatacttgct----gcactctctgttttgattcatgttgttgttattatttgtcattg-ataactgagcatttgtgcggatgttgtattact--tctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
|||| | | | | | | | || ||||| | | || || || || || | |||| | | | | || | | | | ||||||||||||||| ||||| |||||||| | || ||||| || || |||||| || ||||||||||||||||||||||| || ||||| || |||||
gtaaggtcttcacctaatttcattgatattctaatcgaatgcaattcatttattcatttatacataagttactcctccttgggcgcatttttttagtaggcacgcattatcttcatagtttccttccaataggttataacattgcgatccattcctactagcttaattttgttaatttttgcagGTTTTGAGAAGCCATCTGCTATTCAACAGCGTGGTATTGTACCCTTTACCAAGGGCCTCGATGTTATTCAGCAAGCACAATCAGGGACTGGCAAGACTGC
upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 3
cttgaatacttgctgcactctctgttttgattcatgttgttgttattatttgtcattgataactgagcatttgtgcggatgttgtattactt---ctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
||| || || || || ||| || ||| | | | | | ||||| | || | || | | | || ||| ||||||||||||||| ||||| || ||||| | || || ||||| ||| |||||| |||||||| ||||| ||||| || ||||||||||| || || ||
-ttgcatgttttgtgggtgct-tgtggtg-ttcgtagtttcctaccgagaaccaattgaaccgcactctgctgctctaatctcattctggttgacctgtacagGTTTTGAGAAGCCATCTGCTATCCAACAGCGTGGAATCGTTCCCTTCACCAAGGGTCTTGATGTCATTCAACAAGCCCAGTCTGGAACTGGCAAGACAGCMapped 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|254324362|gb|GR833787.1|GR833787EST: TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATACG GTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
genomic: TGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATACGgtatgttcat ... ttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttgtcattgataactgagcatttgtgcggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
tgataac putative branch site (score: 2)
ttacttct putative PPT
attgataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgaatacttgctgcactctctgttttgattcatgttgttgttattatttgtcattgataactgagcatttgtgcggatgttgtattacttctgagaagGTTTTGAGAAGCCCTCTGCAATTCAACAAAGGGGGATTGTTCCTTTCTGCAAGGGGCTTGATGTTATTCAGCAAGCACAATCTGGAACTGGAAAAACTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - tacttgc
- - - - - - - -cactctc
- - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - -gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcggatg