Sequence
atgc intronic sequence ATGC exonic sequence...tgaaagagaatggattggaacttcaaacttctgcttatactctttgttgtgattatatccattgtatgttctcatgtacaaaattatatatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
Basic information
species | Glycine max |
transcript | GLYMA18G16300.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------------------tgaaagagaatggattggaacttc--aaacttctgcttat-actctttgttgtgattatatccattgtatgttctcatgtacaaaattatatatgttttgt-----------agGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
| | | | | || | | |||| || | || | || | ||| || | | ||| || | || ||| |||||| ||| | |||||| || ||||| || |||||||| || ||||| |||| || ||||| ||||||||||||||||| ||||| || ||||| ||| ||||||| || ||
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
--tgaaagagaatggattggaacttcaaacttctgcttatactctttgttgtgattatatccatt-gtatgttctcatgtacaaaattatatatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
|| | | | | | | | ||| | || ||||| | || | | ||| | || | | ||| || || | | || |||||| ||||||| |||||| |||| || |||| ||| ||||| || ||||| ||||| |||||||||||||| || ||||||||| | ||||| || ||
gttgcgttaaatttggcccaactgtttcatttcagtata-actctattctgaagtgtcttgtatttatctgatatt-tgtcttggataat-tgtattaaacagGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA
upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
tgaaagagaatggattggaacttcaaacttctgcttatactctttgttgtgattatatccattgtatgttc-tcatgtacaaaattatatatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
| ||| | | | | | || || | | | | | || | || | || || | || | | | | ||| ||| | ||||| |||||| ||||||| ||||||||||| || || ||||| || || || ||||||||||| || ||||||||| |||||||||| ||
-aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------tgaaagagaatggattggaacttcaa-acttctgcttatactcttt------gttgtgattatatccat-----tgtatgttctcatgtacaaaattata-tatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
| ||| || |||| || | | | || | || | | ||| || ||| ||| ||| | | | | ||| | | | | ||||||||| || ||||| |||||| | || || ||||| ||||||| ||||| ||||||||||| ||||| ||||| || ||||| ||| ||||||| || ||
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------tgaaagagaatggattggaacttcaaacttctgctta-------tactctttgt-tgtgattatatccattgtatgttctcatgtacaaaattata-tatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
||| | | ||| | || | | || || | |||| | || || || | | | | ||| | |||| | | | | ||||||||| || ||||| |||||| | || || ||||| ||||||| ||||| ||||||||||| ||||| ||||| || ||||| ||| | ||||| || ||
gtatgtatctggcttattccttaatgattggagcactaacttctgtttaggattcacctttttttcttaagcaaataatcgtgtatcatatgagggcgcatgatgttctcctgtatttatttgtgtagcttaggcatcctttaaatagtatcatggaaatgttgaatcttaaagtaaacaattctgctttctactgtagGGTCTCTTCCTCTCCCATGGGCTATCAGAATGAAGGTTGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTA
upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
-tgaaagagaatggattggaacttcaaacttctgcttatactctttgttgtgattatatccattgt----atgttctcatgtacaaaattatatatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
|| | | ||| ||| | ||| | || | ||||| ||||| ||| | | |||||||| | |||| ||||||| |||| |||| |||||||||||| |||| |||||||||||||||||||| ||||| ||||||||||| |||||||| |||||||| ||| | ||||| |||||
atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgttttctcatgataacaattttatatgt-----agGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATAMapped 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|192329814|gb|FK023010.1|FK023010EST: AGTATATGAATTTATGCCTCGGGGAAGCCTGGAAAATCACTTGTTTAGGA GGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTG
genomic: AGTATATGAATTTATGCCTCGGGGAAGCCTGGAAAATCACTTGTTTAGGAgtaagttact ... tgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTG
EST:
gi|22523057|gb|BU081868.1|BU081868EST: AGTATATGAATTTATGCCTCGGGGAAGCCTGGAAAATCACTTGTTTAGGA GGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTG
genomic: AGTATATGAATTTATGCCTCGGGGAAGCCTGGAAAATCACTTGTTTAGGAgtaagttact ... tgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtgattatatccattgtatgttctcatgtacaaaattatatatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
atgtacaaaattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaaagagaatggattggaacttcaaacttctgcttatactctttgttgtgattatatccattgtatgttctcatgtacaaaattatatatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- aaagagaa
- - - - - - - - - - - - - -cttctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtac