Sequence
atgc intronic sequence ATGC exonic sequencegttggcctatttctctgcagatttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
Basic information
species | Glycine max |
transcript | GLYMA17G01360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 4
------------------------gttggcctatttc-tctgcagatttgctataaagattgatcatatgaactcttg--tactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
|| ||||| || || ||| | || | | | | ||| || | | || || ||| | | | | | | || ||||| || ||||||||||| || || | || || || ||||| || |||||||| |||||||| ||||| || |||||||| |||||||| |||||||||
gtatatctttgcgcttttatgtgcaaatgcttatttaatccctttatctgcctttcagggtatttggctattttgttgcctagtttcactagcattttcttattttaaattctgtcatgtatttgagcagTTCAAGCAAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGT
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
--------------gttggcc-tatttctctgcagat--ttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
||||| | ||| | | || || || | ||| || | | || || | || || | ||| | | || | | ||| ||| |||||||| ||||||||||| || | | ||||| || ||||| || |||||||| |||||||| ||||| || ||||| ||||| |||||||||| |||
gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaata-cctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
gttggcctatttctctgcagatttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
|||| ||||| | || | || |||||| | || || | || || | ||| | || | | ||||| ||||||||||||||||||||||||| ||||||| || ||||| || | || ||||| ||||||||||| || ||||| ||||| ||||| ||||||||
gttgaa-tatttttttgtggtttga----aaagatatttgttactgcttccaaagcctctatt--tcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 4
gttggcctatttctctgcagatttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
|| | | ||| ||| | ||| ||| | | || | ||| || | || | | | ||| | | | |||||| ||||||| ||||||||||| || || ||| | || || || || ||||| || ||||||||||||||||| || || ||||| || ||||||||||| |
gtagaaatgtttttcttaatgttttgtatggcg------cgcattgatgcttttatcgatggacttagtta--tattcagtttggtacattttgt------agTTTAAGCAAGCTGAAGAGACTGTTACAAAGATGGATTTAGATGGTCTTGTGGTAATTGGTGGAGATGACTCCAATACTAATGCTTGTCTCCTTGCTGAAC
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
gttggcctatttctctgcagatttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
|| |||| | | || | | ||||| |||||| || || ||| ||| | |||| | | | | ||||||||||||||||||||||||| |||||| || ||||| ||||| |||| ||||||||||||||||| ||||||||||| ||||| ||||||||
--------------gtg-agatacacactcaatacatgt-atatgg-ttcttgtggatttgtttttcatcatttattttctgagttttaatggactttt-cagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 4
gttggcctatttctctgcagatttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
|| | | | || || | || | || || | | || ||||| | | ||||| || ||||| ||||| || | |||||| |||||||||||| |||| ||||||||||| || ||||| ||||| ||||| ||||| ||||| |||
---------------------------------gtttcttgtgttt-ttccaatagcagta-atggctctcagctcaatcaatgtgtt--tttgcctttgcagTTCAAGCAAGCGGAAGACACGGCTGTGAAGCTCGACTTGGACGGCATTGTAGTTATTGGTGGGGACGACTCCAACACGAATGCCTGCCTTCTTGCGGAGT
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ12684 (Selaginella moellendorffii), 3'ss of exon 4
gttggcctatttctctgcagatttgctataaagattgatcatatgaactcttgtactattacacat--cttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
| || | || | || | || || || | | || ||| | | | ||||| || ||||| ||||| || | |||||| |||||||||||| |||| ||||||||||| || ||||| ||||| ||||| ||||| ||||| |||
-------------------------------------gtttcttgcgtttttccaatagcagtaatggctctcagctcaatcaatgtatt-tttgccttttgcagTTCAAGCAAGCGGAAGACACGGCTGTGAAGCTCGACTTGGACGGCATTGTAGTTATTGGTGGGGACGACTCCAACACGAATGCCTGCCTTCTTGCGGAGTMapped 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|254330861|gb|GR842126.1|GR842126EST: GTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG TTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTT
genomic: GTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAGgttggcctat ... gcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
taatttattttgcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggcctatttctctgcagatttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG