Sequence
atgc intronic sequence ATGC exonic sequencegtacttatacatgataaaatatataatttgtgttgatgaacaaaaaatacaaccctacattttatgcaggtatctgtagtttatactgtttacttattctgaacactggttttgtttcttcctttcggcaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTGTTGAGGTGGTCCGA
Basic information
species | Glycine max |
transcript | GLYMA20G33300.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g39690.1 (Oryza sativa), 3'ss of exon 6
gtacttatacatgataaaatatataatttgtgttgatgaacaaaaaatacaaccctacattttatgcaggtatc-tgtagtttatactgtttacttattctgaacactggttttgtttcttcctt-----tcggcaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTGTTGAGGTGGTCCGA
| || || || | | | || || |||| || | | ||| | | | | | ||| || || || ||| || || | |||||| |||| || | || ||| | ||||| ||||||||||||||||||||| ||||||||||| || |||||||| |||| | || || ||||| || | ||||| ||||| || |||||||| |||||
----------gtttgaactcatgcttttcttctgaaataatgaataataggtccatgtagtttgttcttctctaatacagtata-acagt--actaatgatgg---tttgttttgcctctttgttgggggttggggtgttg-actttctatcagATGTGGGCACATGTGCACATGTTCAAAATGCGCGAATGAGTTGGTTCGAAGCGGAGGGAAATGCCCGCTGTGCCGTGCACCCATAATTGAGGTGATCCGA
upper sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g57750.2 (Oryza sativa), 3'ss of exon 5
gtacttatacatgataaaatatataatttgtgttgatgaacaaaaaatacaaccctacattttatgcaggtatctgtagtttatactgtttacttattctgaacactggttttgtttcttcctttcggcaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTGTTGAGGTGGTCCGA
| | | | | || | | | || | | | || | | || || | || || || |||| || || || | | | |||||| ||||||||||| ||||| ||||||||||| || ||| ||||||| ||||||| ||||| || |||||||||| || || | |||||||| ||
-----------------------------------gtcagcttcacagctaaacatgtctgatactttgatgttactaatctcta------accttttttgtctgatgtacttgtaaaacccatttggtga--------tggtgacagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG
upper sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G006965_T01 (Zea mays), 3'ss of exon 6
gtacttatacatgataaaatatataatttgtgttgatgaacaaaaaatacaaccctacattttatgcaggtatctgtagtttatactgtttacttattctgaacactggttttgtttcttcctttcggcaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTGTTGAGGTGGTCCGA
|| ||| || | ||| | |||| || | | | | | | ||| || || | || | | | | || || ||| | || | | | |||||||||||||||||||||||| || ||||| || || || || |||| ||||| || ||||| || || ||||| ||||| || | ||||| |||||
-----------------------------gt-ttggctcgcattgaccacattctattatttattggacgagtgt-tgaatcata--gtctatatgtt---ggtagtagctgtgaacctgttttttgt--gtttattactgat--cagATGTGGGCACATGTGCACTTGCTCGAAATGCGCAAACGAATTGGTTCGAGGTGGAGGGAAATGCCCGTTGTGCCGCGCACCCATAATCGAGGTCATCCGA
upper sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
------------------gtacttatacatgataaaatatataatttgtgttgatgaacaaaaaatacaaccctacattttatgcaggtatctgtagtttatactgtttacttattctgaacactggttttgtttcttcctttcggcaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTGTTGAGGTGGTCCGA
|| ||| | | | || ||| ||| | || || || || | | | ||| || | || || || | | || | || | | || || ||| || || ||| |||||||||||||||||||||||||||||||||||||| |||||||| |||||||||| || || || || || |||||||| || ||||||||||| |||||
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttat---cagaac------ctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatct--ttactgtcttccgttgaaaaaaaatg---tgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGAMapped 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|33389021|gb|CA852228.1|CA852228EST: GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTACAG ATGTGGGCACATGTGCACTTGTTCGAAATGTGCCAATGAGTTAATTCGTGG
genomic: GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTACAGgtacttatac ... tttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGG
EST:
gi|15337271|gb|BI497927.1|BI497927EST: GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTACAG ATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGT
genomic: GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTACAGgtacttatac ... tttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattctgaacactggttttgtttcttcctttcggcaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTGTTGAGGTGGTCCGA
tttcttgc CT-rich tract
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttatacatgataaaatatataatttgtgttgatgaacaaaaaatacaaccctacattttatgcaggtatctgtagtttatactgtttacttattctgaacactggttttgtttcttcctttcggcaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTGTTGAGGTGGTCCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG