Sequence
atgc intronic sequence ATGC exonic sequence...gaatgtcttttggatccaggcttgaaacatatcaatagtagtcccttcattttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
Basic information
species | Glycine max |
transcript | GLYMA10G33680.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 3
---gaatgtcttttggatccaggcttgaaacatatcaatagtagtcccttcattttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
|| || | | || | ||| || ||| | || || || | | || || || ||| | || | | || |||| || | ||| |||||||||||||| ||||| || || ||||| ||||| |||||||| || ||||| |||||||||||||||| | | || ||||
gttatgtgagattgcttttttagttttttatggatctttaacagtacatt--ttgggagttatcatgcaaacaat-gttgagctcaatataactatgttgcagGGACGCACTGTTGTTATTGAGCAAAGCTTTGGTGCTCCTAAAGTTACAAAGGATGGAGTTACTGTTGCCAAGAGCATTGAATTCAGTAACAGGGTTAAGA
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 3
----gaatgtcttttggatcca-ggcttgaaacatatcaatagtagtcccttcattttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
| ||| | |||| | | ||| | | | || | | | || | ||||| | | || |||| || || | |||| || ||||||||||||||||| || | ||| |||| ||||| ||||| || || || || ||||| ||||||||||| |||||||||| ||||||||
agcacagtgtttgttgggcctacaactttttatgtttttattttg---tcagagtgctgtgttgtgttatttgcag--attggacttaacgtgtctattatgcagGGACGCAATGTGGTTATTGAGCAGAGCTATGGTTCACCGAAAGTCACAAAGGACGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAGTCAAGA
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 2
---gaatgtcttttggatc--caggcttgaaacatatcaatagtagtcccttcattttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
| || | | || ||| | | | ||| | | | || ||| | | | ||| || | | || | |||||||| |||||||||||||||||||| || || ||||| ||||| ||||| ||||| || || ||||| |||||||||||||| ||||||| ||| ||||
actcactgattccaatactgtttggtttgttttactttgtt-gtaatactgttgccttagttgtttgtt-ttgtacttgaacttatcgcctgc---cttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
--gaatgtcttttggatccaggcttgaaacatatca----atagtagtcccttcat-tttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
|| | |||||| | | | ||||| | | ||| || || ||| | || | |||||| || | | ||||||| |||||||||||||||||||| ||||| ||||| ||||| ||||| ||||| || || || || |||||||||||||| ||||||| ||| ||||
gcactcactgattataatattgcttgatgtgctttactctgttgtagtactgttgcatttagtttgttttgtacttgaat-ttattgcctgctt------tctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------gaatgtcttttggatccaggcttgaaacatatcaatagtagtcccttcattttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
|| | | || | | |||| | |||||| | | ||| || || | | | | | | ||| ||||| |||| |||||||| | || || ||||| | || ||||| || |||||||| ||||| || || ||||| ||||||||||| |||||||||| | | ||||
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgaccta---ttgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaacc---atttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------gaatgtcttttggatccaggcttga-----aacatatcaat--agtagtcccttcattttg-attggtgttgatc-acgattgttattgttaaattggtgt--ttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
| | | ||||| ||| | | ||| | | | || | || ||| || || | ||| || | || | | ||| | | | |||| |||| |||||||| || ||||||||||||| || || || ||||||||||||||||| || || ||||| || || ||||| ||||| || ||| | ||||
gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGAMapped 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|192326928|gb|FK015155.1|FK015155EST: AGGGTGTTGAAGAGCTCGCCGATGCCGTCAAAGTAACCATGGGCCCTAAG GGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAA
genomic: AGGGTGTTGAAGAGCTCGCCGATGCCGTCAAAGTAACCATGGGCCCTAAGgtaaccaagc ... gtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAA
EST:
gi|213593632|gb|DB971654.1|DB971654EST: AGGGTGTTGAAGAGCTCGCCGATGCCGTCAAAGTAACCATGGGCCCTAAG GGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAA
genomic: AGGGTGTTGAAGAGCTCGCCGATGCCGTCAAAGTAACCATGGGCCCTAAGgtaaccaagc ... gtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcattttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
tgttgat putative branch site (score: 4)
tgttttt putative PPT
attgttattgttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatgtcttttggatccaggcttgaaacatatcaatagtagtcccttcattttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - cttttgg
- - - - - - - -ccaggct
- - - - - - - - - - - - - -catatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg