Sequence
atgc intronic sequence ATGC exonic sequencegtcattatatttctctgcttgttgtgaataggtaaaacctctgaattcttgacacaatgccttgcatttttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
Basic information
species | Glycine max |
transcript | GLYMA06G02120.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G02120.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g04100.2 (Oryza sativa), 3'ss of exon 5
----------------gtcattata--tttctctgcttgttgtgaataggtaaaac-ctctgaattcttga-cacaa--tgccttgcatttttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
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gggtaccaactatatagaaagtatagattagttaataaatgaccatctagcacaacattgtaaactgtagatcataacatgatttacattgtgcaa---acagCAATCTTGCAAGAATAGAGAGGAGCGCTGAAAAGCAAGCGAAATCAGGAGCAGAAAATGCTGGGTGGTATGAAAAATG
upper sequence: GLYMA06G02120.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G126812_T01 (Zea mays), 3'ss of exon 5
----------gtcattatatttctctgcttgtt------gtgaataggtaaaacctctgaattcttgacaca-----atgccttgcatttttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
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tgccatatgtgtcagtttcttctttgatgtccttccaaagttagaacttagaacaattgtacaagggagacactgatatggtttaccttgtccaat--acagCAATCTTGCAAGAATAGAGAAGAGTGCTGAAAAACAAGCAAAATCAGGTGCAGAAAATGCTGGGTGGTATGAGAAATG
upper sequence: GLYMA06G02120.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G42430.2 (Arabidopsis thaliana), 3'ss of exon 5
------gtcattatatttctct-----------gctt-gttgtgaataggta--aaacctctgaattcttgacacaatgcc-ttg-cattttta--aatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
|| || | ||| | | |||| |||| || || | | || |||||| | | ||| || || | || || |||||| ||||||| || ||||| ||||||||||| ||||||||||||||||||||||||||||| ||||| || |||||
gtctatgttataacattccctttaccagatatagcttcgttgccaacagttttcgcgctgctagattcttacagtcctctcattgtcaacttgatcaaatttcagTAATCTAGCAAGGATTGAAAGGAGTGCACAAAAGCAAGCAAAATCAGGAACTGAAAATGCTGGTTGGTACGAGAAATG
upper sequence: GLYMA06G02120.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g02700.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------------------gtcattatatttctctgctt----gttgtgaataggtaaaacctctg--aattcttgacacaatgccttgc-atttttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG----------------------
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gtcttgtctttattattgtgtactgcacttaaagataacttctgatttttgcaaacacaactgtaagcacaaattaaagttttatggtttagcatgggcacaatttgtagtaattgtggatactataattaccgaattttaaatttgtagTAATCTAGCTAGGATAGAGAGGAGTGCACAAAAACATGCAAAATCTGGCACCGATAATGTTGGGTGGTATGACAAGTGGCAAGGAAATCATTCACTGTCCMapped 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|151409651|gb|EV279459.1|EV279459EST: GATACTTGGTGGGAAACATGGCAGGAAAATCTTCATCAAGATGAATGGAG TAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAAC
genomic: GATACTTGGTGGGAAACATGGCAGGAAAATCTTCATCAAGATGAATGGAGgtcattatat ... aaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataggtaaaacctctgaattcttgacacaatgccttgcatttttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
tcttgac putative branch site (score: 3)
ttgcatttttaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcattatatttctctgcttgttgtgaataggtaaaacctctgaattcttgacacaatgccttgcatttttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA