Sequence
atgc intronic sequence ATGC exonic sequence...aggtgatgcagtatatacttatatggacctgagttcctgttctttataaaatttattactttttttatcataaagattaattttgttgttattttggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
Basic information
species | Glycine max |
transcript | GLYMA19G43540.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43540.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g42900.1 (Oryza sativa), 3'ss of exon 5
---aggtgatgcagtatatacttatatggacctgagttcctgttctttataaaatttattactttttttatcataaagattaattttgttgttattttggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
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gtcagtttttgttgcactttgagctaaacacgatagtactt-ttatctttaaaat--gctaattcacgaggca--gctactgatat-gtgcatccgtcaaaagGTTACACACAACATGCAAATTCCTCTCTCCTATGCTGATGCTGTGATTGGAGCAGCTGGTGCTAGTATTAGCTATATTCGTAGGCACAGTGGTGCAACAG
upper sequence: GLYMA19G43540.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G130095_T02 (Zea mays), 3'ss of exon 3
aggtgatgcagtatatacttatatggacctgagttcctgttctttata-aaatttattactttttttatcataaagattaattttgttgttatttt-----ggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
|| | ||| | | || || || | | || | | | | ||| | | | | || | |||| ||| || ||| | ||| | || || |||||| ||||||| || |||||||||||||| || || ||||||| || ||||| ||||||||| | | |||||| || |||
--gttagtttgtacacatttgactgctactaatatgatgaattatttgcatgcctatctcatgatcagttgtacttaacttttttcttggtaattttatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGGGCAGCTGGTGCCAGTATCAGCTACATCCGCAGGCATAGTGGAGCAACTA
upper sequence: GLYMA19G43540.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G04610.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------aggtgatgcagtatatacttatatggacctgagttcctgttctttata-aaatttattactttttttatcataaagattaattttgttgttattttggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
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gtattccgccaatctctgcaacatgttatgaagttgactgttcaatctactgcaatttatgtatgtaaagtaaatcaatgaaaatctgagtggtgtggg--gatttgtttgtt-ttgcagCAAGTTACGCAGCAAATGCAGATTCCACTGTCTTATGCTGATGCTGTAATTGGGACGTCGGGTTCAAACATAAGCTACACTAGACGTCTTAGTGGAGCAA---
upper sequence: GLYMA19G43540.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0081g00440.t01 (Vitis vinifera), 3'ss of exon 6
-----------aggtgatgcagtatatacttatatggac---ctgagttcctgttctttataaaatttattactttttttatcataaagattaattttgttgttattttggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
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cgaattttggttgaacaagcagtttttgctcactctcacttcctgagt-cctgttccttctaaaa------agtgtttgaactctgaaa--taatctcatt-----ttttgcagGTAACACAACAAATGCAGATTCCTCTGTCTTATGCTGATGCCGTTATTGGAACAGCTGGTGCAAGTATAAGTTACATTAGGCGTGCTAGTGGGGCAACTGMapped 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|151408799|gb|EV278607.1|EV278607EST: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATTGTCACACAG ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATTGTCACACAGgtacttgttc ... attttggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaaatttattactttttttatcataaagattaattttgttgttattttggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
gattaat putative branch site (score: 3)
ttatttt putative PPT
atttattacttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggtgatgcagtatatacttatatggacctgagttcctgttctttataaaatttattactttttttatcataaagattaattttgttgttattttggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
-ggtgatg
- - - - - - - - - - - - - - - - - tcctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtt