Sequence
atgc intronic sequence ATGC exonic sequence...tctgttttttctctcaattttcttcttttgtcaaaagcataaaaaattggaaagaaatattaacaaaataagatatttatgtgttttattgttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
Basic information
species | Glycine max |
transcript | GLYMA17G00830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 1
-----------------------------tctgttttttctctcaat-tttcttcttttgtcaaaagcataaaaaattgga---------------aagaaatattaacaaaataagatatttatgtgttttattgttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
|| | | | | | | || ||| || || ||||| | || | | | | | || | |||| |||||||||||| || ||| |||| ||| | ||||| ||||||||||||||||||| || ||||| ||||||||||| || || |||
gtacgtcctctctctctctctcgcttgctcgtgcagtgtacttgagtgtcgattgtttcacttgaactgaaattaattgtgttccctttttgtttcgcggcgcatgtggcattgggggtggtggtctgctcgtttgtgcgtgcagTTAGTGTGAGCGAGGTTGAGGCGTTGTATGAGCTGTTCAAGAAGATCAGCAGCGCGGTGATCGATGACGGACTGATCAACAAG
upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 2
--------------------------------tctgttttttctctcaattttcttcttttgtcaaaagcat--aaaaaattggaaagaaatat-taacaaaataagatatttatgtgttttattgttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
| || | || |||| || | | | ||| |||| || | | | | | ||| || ||| | ||||| |||||| || || || ||| | || ||||| || || | ||||||||||| |||||||| |||||||||||||| || ||||| |||
gtaagtccgccgcattcgccattggttggggcgccgtactcctccttccttttgttgctgagcctgtctcattgggggaatttgactggtgtgtgtggttgggttggatttt---gtggccttgtgttg-tgcagTCAGCGTGAGCGAGGTCGAGGCGCTGTACGAGCTCTTCAAGAAGATAAGCAGTGCTGTGATTGATGACGGGCTGATTAACAAG
upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
------------------------tctgttttttctctcaattttcttcttttgtcaaaagcataaaaaattggaaagaaatattaacaaaataagatatttatgtgttttattgttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
|| ||| | || |||||| |||| | || | | | | | |||| | | | | | | | || | | | | ||||||||| || || ||| | || || | |||||| |||||||||||||||||||||| ||||||||||| || || || || |||
gtacgtccaagccgcttccccgtttccgttgtctccttcaatt--cttcgtccgt-agtaccgtgatcgattgtcttccgtt--tgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------tctgttttttctctcaattttcttcttttgt-caaaagcata-aaaaattggaaagaaatattaacaaaataagat--atttatgtgttttattgttga-tgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
| | |||||| | | || | || | ||| | ||| | | || ||| | || | | || | || || || ||| || | || |||||||||||| ||||| || ||||| || ||||| | || ||||| ||||||||||| ||||||||||| || ||||| || |||
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 1
tctgttttttctctcaattttcttcttttgtcaaaagcataaaaaattggaaagaaatattaacaaaataagatatttatgtgttttattgttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
||||||||||||| || ||||| || |||||| |||| ||||||||||||||||| || |||||||| || || || || |||
----------------------------------------------------------------------------------------------------ttAGTGTAAGTGAAATAGAAGCACTTTATGAACTGTTTAAGAAGATCAGCAGTGCTGTAATTGATGATGGCCTCATCAACAAGMapped 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|151412447|gb|EV282259.1|EV282259EST: GCAACCTACAGGTTTAGAAAATCCAGAAGTTCTTGCAAGAGAAACAGTGT TTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCA
genomic: GCAACCTACAGGTTTAGAAAATCCAGAAGTTCTTGCAAGAGAAACAGTGTgtatgtcata ... gttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attggaaagaaatattaacaaaataagatatttatgtgttttattgttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
aaagaaatattaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgttttttctctcaattttcttcttttgtcaaaagcataaaaaattggaaagaaatattaacaaaataagatatttatgtgttttattgttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa