Sequence
atgc intronic sequence ATGC exonic sequence...tcttttttcttcctaaaatgtttcttaaaaatgctctcttttgctttatggttgtgcatttccttgtatatatattttaggcatgtttcgctgttaatagGTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTTGACCGAGAAGCTGATGATCTTGCTGTACGTATTGCTTTGGGAGAGACTC
Basic information
species | Glycine max |
transcript | GLYMA13G09970.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G09970.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g52200.1 (Oryza sativa), 3'ss of exon 7
-tcttttttcttcctaaaatgtttcttaaaaatgctctcttttgctttatggttgtgcatttccttgtat-atatattttaggcatgtttcgctgttaatagGTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTTGACCGAGAAGCTGATGATCTTGCTGTACGTATTGCTTTGGGAGAGACTC
|| ||||| || || || | ||| | | | | | | ||||| || || | ||||||| |||||||| || |||| ||| | ||||||||||| |||||||| ||||||| ||||| |||||||| ||||||||| | || ||||| |
atcctttttagggttaggatagttttgctgaattttgaaaaaaaaaaaacaatcaaac--tctcgtgtatcatgctaaccgatcaaactcattcacatttagGTTGCTGAAAACATAGCAAGGAAGAATGGAATCAGTAAAAGTGAATTACTTGATAGAGAAGCAGATGACCTTGCTGTTCGTATTGCTCTTGGTGAGACAC
upper sequence: GLYMA13G09970.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G031529_T01 (Zea mays), 3'ss of exon 6
---------------------------------tcttttttcttcctaa---------aatgtttcttaaaaatgctctcttttgctttatg--gttgtgcatttccttgtatatatattttaggcatgtttcgctgttaa----------------tagGTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTTGACCGAGAAGCTGATGATCTTGCTGTACGTATTGCTTTGGGAGAGACTC
| |||| ||| | ||| | || | ||| | | | | | ||| | | | | | || | | | |||||| | || |||||||| ||||||||||| |||| |||| | ||||| ||||| ||||| || ||||||| |||||||||||||| ||||||||| | || ||||| |
gtatggttctctcacatatttgacatcaactgtttttttgtctgttcagtgtcaactcaatactcctctgatatgttgtttctgagataatgtagatagatactggcccacatgatcttgtcaagcatgtctaatgattgggctctgctttttcgtttagGTTGTTGAAAACATTGCAAGGAAGAATGGTATCAGTAAGAGTGAGTTACTCGATAGAGAAGCAGATGATCTTGCTGTTCGTATTGCTCTTGGTGAGACAC
upper sequence: GLYMA13G09970.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G19610.1 (Arabidopsis thaliana), 3'ss of exon 7
tcttttttcttcctaaaatgtttcttaaaaatgctctcttttgctttatggttgtgcatttccttgtatatatattttaggcatgtttcgctgttaatagGTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTTGACCGAGAAGCTGATGATCTTGCTGTACGTATTGCTTTGGGAGAGACTC
| || ||||| | | || ||||| |||| | || | | | | | || | | |||| ||| |||| ||| || | |||||||| | | || | |||||| || || ||||| ||||||||||| |||||||| |||| ||||||||| ||||||||||||| ||
-gtacgtttttcctg-------tttaaagaatgcatcctttagtgttttttaaatatagcttgcttcatgttttttttcttttcctttttgtgttg-tagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTTGACCGTGAAGCTGAAGATCCTGCTGTACGCCTTGCTTTGGGAGAAACAA
upper sequence: GLYMA13G09970.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0011g01060.t01 (Vitis vinifera), 3'ss of exon 7
--------tcttttttcttcctaaaatgtttcttaaaaatgctctcttttgctttatggttgtgcatttccttgtatatatattttaggcatgtttcgctgttaatagGTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTTGACCGAGAAGCTGATGATCTTGCTGTACGTATTGCTTTGGGAGAGACTC
||| ||| | ||| | ||| || ||| || ||| | || | | ||| ||| | ||| | | | | |||||||||||| ||||| || || |||||| |||| | ||||||||||||||||||||| | |||| |||||||| || ||||||||||| |||||||| ||||
tattcatgtctgccttcctt-taataagttgtttc----tgcattcacttgatggtctattctaaaattctttgccc---tgatttccatttctctgtatattaatagGTTGTTGAAAATATCGCTAGGAAATATGGTATAAGTAAAAGTGATTTACTTGACTCACAAGCCGATGATCTCGCCGTACGTATTGCATTGGGAGAAACTCMapped 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|254313854|gb|GR831483.1|GR831483EST: AGCATGGAATAGTCTGTTCATGCGCTCTGATACT GTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTT
genomic: AGCATGGAATAGTCTGTTCATGCGCTCTGATACTgtatgtttct ... ctgttaatagGTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatggttgtgcatttccttgtatatatattttaggcatgtttcgctgttaatagGTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTTGACCGAGAAGCTGATGATCTTGCTGTACGTATTGCTTTGGGAGAGACTC
tttcgct CT-rich tract
atttccttgtatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttttttcttcctaaaatgtttcttaaaaatgctctcttttgctttatggttgtgcatttccttgtatatatattttaggcatgtttcgctgttaatagGTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTTGACCGAGAAGCTGATGATCTTGCTGTACGTATTGCTTTGGGAGAGACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - ttcttcc
- - - - - - - - - - - - - - -aatgctc
- - - - - - - - - - - - - - - - - - -cttttgc
- - - - - - - - - - - - - - - - - - - - - - - - -ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt