Sequence
atgc intronic sequence ATGC exonic sequencegtatgataataattgatcatttctgtttcatctgcaacccaccctcccacatttttttcaaacgttattttctcttgttataccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
Basic information
species | Glycine max |
transcript | GLYMA20G37210.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g14150.5 (Oryza sativa), 3'ss of exon 1
------gtatgataata-------attgatcatttctgtttcatctgcaacccaccctcccacattt----------------ttttcaaacgtt--------attttctcttgtta-------------------taccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
||| ||||| ||| || | || |||| ||||||| |||| | | | ||| |||| | || | | | ||||| | ||||||| || |||||||||||||| ||||| |||||||||||||||||||| ||| ||| ||||| || |||||||||||||| ||||||||||| |||||
gtaagagtaaaataatgcttctgcattagtcttctcagtttgatctgcagcccagctttcactgtttgggtgatttggggcgcttttaaggtcttccagaagaactgcttagtgttaacttgagttttggaaaaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGTACCGGGGAGTTGACTGCGGTGATGGAGGCCCCTTTGGAGCAGTCGTTGT
upper sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 2
---------------------------gtatgat--aataattga--tcatttctgttt--catctgcaacccac--cctcccacatttttttcaaacg-----ttattttctctt-gttatac----cagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
||||| | ||| | | || | ||| |||||| | | | | | | |||| |||||| |||| | | | |||| ||||| || || || ||||| || || | ||||||||||||||||| ||| | || || || ||||| ||||||| |||||||| |||||||||||
gtattattaccagatttgatcttatggacatgattgaccaatgaatattatatatgtccaacatctgttattttctgctgattggaggactgttaaacactcacttatttaatctttgatgcattaaacagCCGTACAAGACAGGGATCACAAATTTTTGTCTAAAGCAGTTGAAGAAGCTTACCAAGGAGTAGATTGTGGCCATGGAGGTCCATTTGGTGCAGTTGTTGT
upper sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G082924_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------------------------gtatgataataattgatcatttctgtt---------tcatctgcaacccaccctcccacatttttttcaaacgttattttctcttgttataccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
|| | | | | || || | || | || | || ||| | | | | | | | || | ||| | | | |||||||||| || || || ||||| ||||| ||||||||||| |||||||||||| || || || || || |||||||| ||||||||||||||||| ||
gtgagaacattgccatggtatttttttttgtagttccctcgtagttgcacagctttacttactgagataaggtcaacactggacatggcctggacctatgatctctaaggtcacagtttctcgcctttggtaaaacttgctcttatgtaacgacagcaagaaaactgatctaagacctgcattttggtgaattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCATACCGAGGAGTCGATTGCGGCGATGGAGGTCCATTTGGAGCAGTTGTCGT
upper sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------gtatgataataattgatcatttctgtttcatctgcaaccc---accctcccacatttttttcaaacgttattttctcttgttataccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
| ||| | | |||| |||| ||| | | || | | | || | | | | || || | | ||||||| || || || |||||||| || ||| |||| ||||| || ||||||||| || ||||| || || |||||||| |||||||| |||||||||||
gtgacattgttgcttcctcgtccactaaactctatattgtcttgtccccatttcatcgcatgcatggcattcaagattcaactaatacaacctatgcattcctgtacacactgttattccttactgtgaaaaaggacttgcttatttgagctttggtttatcaaacagCTGTGCAAGACAGGGACCACAAATTTTTATCAAAGGCAGTGGAGGAAGCATACCGAGGAGTTGACTGCGGCGATGGAGGACCATTTGGTGCAGTTGTTGT
upper sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------gtatgataataat-tgatcatttctgtttcatctgcaacccaccctc---------ccacattttttt-caaacgttatt-----ttctcttgttatac------------cagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
| | || | | | |||| || || || || ||| || || | ||| || | ||| || || | || ||||| ||||||| || ||||| ||||| || ||| |||| |||| ||||||||||| |||||||| || || ||||||||||| ||||||||||| || || ||||
gtaatagaccttatgacttatagtgatgacttatgatcactgtgatgcttatacctttggctttgtaattttgctcttgctatttttgatttatgtgtccaccattcttagttgaagattgtatgtgtttgcagaagttgttgtggtttatgtttctatactttgtctttgatcagCTGTTCACGATAGCGACCATAAATTCCTAACGCAAGCTGTTGAAGAAGCTTACAAGGGAGTGGACTGTGGTGATGGTGGCCCATTTGGTGCGGTGATTGT
upper sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0030g01610.t01 (Vitis vinifera), 3'ss of exon 2
-gtatgataataatt--gatcatttctgtttca-tctgcaacccaccctcccacatttttttca--aacgttattttctct--------tgttataccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
| | ||| ||||| | | | | | || |||| | || || || | | | | | ||| || | |||| ||||| |||||||||||||||| |||| ||||||||| ||||||||| || ||||| || |||||||||||||| |||||||| ||||| || || ||||||||
tatttaatattaattttgttgaggagggctgcagtctgaagcctacaaaggtggtttatggtagttatcatggtttcctttcgggtgattgttcaaccagTTGTACAGGATAGAGACTACAAATTCTTAACAGCAGCAGTTGAGGAGGCATATAAAGGGGTTGAATGTGGAGATGGAGGTCCATTCGGTGCGGTTGTTGTMapped 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|254317969|gb|GR832137.1|GR832137EST: CAAAGATGGTACTATTTCTGTTGCTTCAGCATTTCCTGGTCATCAAGAAG CTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCAT
genomic: CAAAGATGGTACTATTTCTGTTGCTTCAGCATTTCCTGGTCATCAAGAAGgtatgataat ... gttataccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCAT
EST:
gi|27426215|gb|CA937735.1|CA937735EST: CAAAGATGGTACTATTTCTGTTGCTTCAGCATTTCCTGGTCATCAAGAAG CTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCAT
genomic: CAAAGATGGTACTATTTCTGTTGCTTCAGCATTTCCTGGTCATCAAGAAGgtatgataat ... gttataccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcaacccaccctcccacatttttttcaaacgttattttctcttgttataccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
ttattttctcttgtt CT-rich tract
atttttttcaaacgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgataataattgatcatttctgtttcatctgcaacccaccctcccacatttttttcaaacgttattttctcttgttataccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG