Sequence
atgc intronic sequence ATGC exonic sequencegttagccttttagccattccagttgtatctggaccatctgacgtttactagttggctaagaattaattttctgacataagtaaaaccaatgccttcttttgatgttattttaacttatatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
Basic information
species | Glycine max |
transcript | GLYMA20G28950.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 2
gttagccttttagccattccagttgtatctggaccatctgacgtttactagttggctaagaattaattttctgacataagtaaaaccaatgccttcttttgatgttattttaacttatatctgtc-tactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
| | | || ||||||| | || | | ||| |||||| ||| || | || ||| || |||| || ||||| ||||||| ||||| |||| |||||||||||||||||||| |||||||||||| ||| | ||||| || || ||| | || | |||||||| |||||||
--------------------------------------------------gatagtgccatatccattttct-atatcttattttcgtagattttcctttgattctatggtattgt-cataggtcatattcat--gaagttttgtttg--ccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA
upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagccttttagccattccagttgtatctggaccatctgacgtttactagttggctaagaatta--attttctga--cataagtaaaaccaatgccttcttttgatgttat--tttaacttatat-ctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
|| | || | || ||| | | | | ||| | || | || ||| ||| |||| | | | | ||| || | | | |||| | || ||| || || | || | || | | | ||| ||||||| |||||||| || |||||||||||||| |||||||| ||||||| || ||||| ||| ||||||||||| ||| | ||||||||||| || |
-gtatctttctcatggttttggtttctttttca--aattgaaataagatatggatcatagtatttgcattgcctgaagccttatgataacttattggtatatctcatgtaacaacttttgttagatgctttgtatataacttcttttgttggcgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAAATCGAGACTTTGTCAAGGATTACTCAAATATTGAAAGATGTTATACAAA
upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 2
gttagccttttagccattccagttgtatctggaccatctgacgtttactagttggctaagaattaattttctgacataagtaaaaccaatgccttcttttgatgttattttaacttatatctgtctactcatctagagatttg--taaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
||| || |||||| || | | | ||| || ||||| | || || | | ||| | | || | | | ||||||| || || ||||| |||||| | || ||||| |||||||||||||||||| |||||| || |||||||||||| ||||| | |||||||||||||| |
--------------------------------------------------------caaggat-aattttttggtctcttttacttgaatctgtttatttgaaaattttatactgggcacttcctaactgacatgtttgttgaattggattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAGTGTGAGACTTTAGCAAGGATTACTGCTATATTGAAAGATGTTATTCAAAMapped 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|207709891|gb|GD690575.1|GD690575EST: CTGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAG GATGACAAAAATGTTGCACA
genomic: CTGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAGgttagccttt ... aaatttttagGATGACAAAAATGTTGCACA
EST:
gi|13480887|gb|BG510230.1|BG510230EST: CTGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAG GATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAG
genomic: CTGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAGgttagccttt ... aaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgttattttaacttatatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
ttttaac putative branch site (score: 2)
ttttt putative PPT
tagagatttgtaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagccttttagccattccagttgtatctggaccatctgacgtttactagttggctaagaattaattttctgacataagtaaaaccaatgccttcttttgatgttattttaacttatatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG