Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatagcattttgtgcagtctttgctgagttcatgttctgtgggaacttactgacatgtttgggactaatgctatttttttggcatgctgacacatggaatgaataatacgttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTAT
Basic information
species | Glycine max |
transcript | GLYMA20G32900.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g61950.2 (Oryza sativa), 3'ss of exon 4
gtatg-tatagcattttgtgcagtctttgctgagttcatgttctgtgggaacttactgacatgtttgggactaatgctatttttttggcatgctgacacatggaatgaataatacgttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTAT
||| | | ||| | || ||| | || | | || || || | | | | | ||| | | | | || | | | | ||| ||||||| |||||||||||||| || |||| ||||| ||||| | || ||||| ||||| |||||||| |||||||| | |||||| | |||||||||||
gtaaacttctatactttctcaagcattt--taagaccccttccttaatttgtttgggcgtatagtggaggttcccgtgattact--aata-accgtcatgttgcctctttcata--ttccagACATATGGCAATGGTCAGAGTTAACCGGCTTTGGTGATCTACCATCACCTCGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAAATTGTTAT
upper sequence: GLYMA20G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G351160_T01 (Zea mays), 3'ss of exon 4
gtatgtatagcattttgtgcagtctttgctgagttcatgttctgtgggaacttactgacatgtttgggactaatgctatttttttggcatgctgacacatggaatgaa---taatacgttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTAT
| || |||| || | | | | | | || || || | | || || | || ||||| |||| | | ||| ||| ||| ||||||||||||| || | |||||||| ||||| || || ||||||||||| |||||||| |||||||| | |||||| | || ||||||||
--------------gtaagc-gtctatgtttcatcatcaaattttcaaagcccccttctctggttctgtttg-cacttgttctaggggttgctgctacattcatgatacttctgtacattc-agACTTATGGCAATGGTCGGAGATGACTGGCTTTGGTGATTTACCGTCACCACGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAGAAAGATTGTTAT
upper sequence: GLYMA20G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G468485_T01 (Zea mays), 3'ss of exon 2
gtatgtatagcattttgtgcagtctttgctgagttcatgttctgtgggaacttactgacatgtttgggactaatgctatttttttggcatgctgacacatggaatgaa---taatacgttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTAT
| || |||| || | | | | | | || || || | | || || | || ||||| |||| | | ||| ||| ||| ||||||||||||| || | |||||||| ||||| || || ||||||||||| |||||||| |||||||| | |||||| || ||||||||
--------------gtaagc-gtctatgtttcatcatcaaattttcaaagcccccttctctggttctgtttg-cacttgttgtaggggttgctgctacattcatgatacttctgtacattc-agACTTATGGCAATGGTCGGAGATGACTGGCTTTGGTGATTTACCGTCACCACGAGAGTTTGCTGCTGCTTCAGCCATAGGAAACAAAAAGATTGTTAT
upper sequence: GLYMA20G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G36360.5 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtatagcattttgtgcagtctttgctgagttcatgttctgtgggaacttactgacatgtttgggactaatgctatttttttggcatgctgacacatggaatgaataatacgttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTAT
| ||| || | | |||| | || || | | | | ||||| ||| | || | | | | ||||| ||| || | | | | ||||||||||||| ||||||||| | ||| ||||||| ||||| ||| |||| || ||||||||||| ||| | || |||| |
--------gtaagttttaacaatgtcgtgtgagacc-tgccttggatttattaatactctgctttggcacttctatgatatctcta--ttcatgacagATG---CTAACATT-TGCTGCAGATATATGGCAGTGGTCTGAATTGACTAGCTTCGGCGACTTACCTACACCTCGTGATTTTGCTGCCGCTGCTGCTATTGGGA----------------
upper sequence: GLYMA20G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G36360.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtatagcattttgtgcagtctttgctgagttcatgttctgtgggaacttactgacatgtttgggactaatgctatttttttggcatgctgacacatggaatgaataatacgttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTAT
||| |||| | ||| || | | |||| | || || | | | | ||||| ||| | || | | | | ||||| ||| || | | | | ||||||||||||| ||||||||| | ||| ||||||| ||||| ||| |||| || ||||||||||| ||| | || |||| | || |||||||| |
gtacgtatgtaagttttaacaatgtcgtgtgagacc-tgccttggatttattaatactctgctttggcacttctatgatatctcta--ttcatgacagatg---ctaacatt-tgctgcagATATATGGCAGTGGTCTGAATTGACTAGCTTCGGCGACTTACCTACACCTCGTGATTTTGCTGCCGCTGCTGCTATTGGGAGCCAAAAAATTGTGTT
upper sequence: GLYMA20G32900.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0074g00620.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------gtatgtatagcattttgtgcagtctttgctga-gttcatgttctgtgggaacttactgacatgtttgggactaa-tgctatttttttggcatgctgacacatggaatgaataatacg-ttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTAT
|| | || || ||| |||| || | || ||| | | | || || | ||| | | || | || | | | | | ||| |||||||||||||||||||||| || || || | || |||||||||||||||||| | |||||||| || |||||||| |||||||||| |||||||||||
gtaagacatttttaacattttaaaaaatgcataaggattatatgttgccttaaatttggagatgagcaggttttatttaactatagcctttcgtatttatttaactatgggctccatgtcttgttaagggctaattgaatttatattcttccagATATATGGCAATGGTCAGAGCTGACCAGTTTTGGTGACTTGCCTTCACCAAGGGATTTTGCAGCTGCTTCAGCTATTGGAAACCGGAAAATTGTTATMapped 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|22930245|gb|BU547384.1|BU547384EST: GTTGGGGGACTTTTGGGTTTTGGATACTG ATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCAC
genomic: GTTGGGGGACTTTTGGGTTTTGGATACTGgtatgtatag ... tacgttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggactaatgctatttttttggcatgctgacacatggaatgaataatacgttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTAT
tgctgac putative branch site (score: 2)
aatgctattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatagcattttgtgcagtctttgctgagttcatgttctgtgggaacttactgacatgtttgggactaatgctatttttttggcatgctgacacatggaatgaataatacgttccagATATATGGCAATGGTCTGAACTAACTGGCTTCGGTGACTTGCCTTCACCACGAGATTTTGCTGCAGCTTCAGCAGTTGGAAACCGTAAAATTGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT