Sequence
atgc intronic sequence ATGC exonic sequencegttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
Basic information
species | Glycine max |
transcript | GLYMA19G00260.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 5
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccact--gtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
||| || ||||| | ||| | | || | || | || || ||| || || || | | | | | | || || || | |||||| || |||||||||| ||||| || || | |||||||||||||| ||||||| ||||||||||| ||||| |||||||| | || || || ||
----------------ctta-caagttttggtaattgc-acatttacatttgtacctatgtgcatcacgtgttgacgtttacattttaattgaattgact-tctgtttcattggc------------acagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT
upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G077125_T01 (Zea mays), 3'ss of exon 5
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
| | | || |||| ||| | | | |||| |||| || | | | || |||| ||| | |||| | | | || | |||||| || |||| ||||||||||| || || || ||||| |||||||| |||||||| ||||| ||||| ||||| |||||||| | || || || ||
----------gaat-ctcagtccagtttgtttcacttcatatgtgcttgcgggtccttt--------cggtcagaat--tcacataaaaataatgga-gcatttcatgttttctttaca-------cagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTATGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G078826_T01 (Zea mays), 3'ss of exon 5
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
|| | | ||||| ||| |||| | | | ||||| |||| | | | | || ||| | |||| || | || |||||| || |||| ||||||||||| || || || ||||| || ||||| |||||||| ||||| ||||| ||||| |||||||| | || || || ||
-----------cttagtccagtttgtttcattttatctgtg--cttttgtgggtcctttttttgtcagaatttgcatcaacacggtgaagcgccttttgttttct----------------ttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 7
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
| ||| | | || | | | | || || || | | |||||| | | | | ||| |||| ||| | | || ||||| ||| || || ||||| ||||| | ||||||||||| ||||||||||| || ||||| || |||||||||||||| ||||| | || | ||| |||
----------------------gtatttatataatccaaatcctc----ccagtcctgtaaaacaaatgattaaattat-----gtgacttgatgattatattagctaatacgatttgagat--cacagGGCGGTCGTAAACTATGATTTCCCCAATGGAGTGGAAGACTATGTTCATAGAATCGGAAGAACAGGAAGAGCTGGAGCGACTGGTCAGGCATTCACATTC
upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G14610.2 (Arabidopsis thaliana), 3'ss of exon 7
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttac-aatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
| | | | | | | || || | | | | || | | ||| | | |||| | | | || ||||||||| ||||| ||||| || || | ||||| || |||||||| ||||| |||||||| ||||||||||||||||| || || ||||||||||| |||
------------------------------------------------gtatgaatatgattc-cagtttcaaattcaaccatcagaattatagaagcatatgatccgaatgtagaaatttgattcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC
upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatatt-ttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
||| | | | ||| | || | | || | || | | | | ||| | |||| | | | || || ||||||| | | || | |||||||||| |||| ||||| ||||| || ||||| || |||||||| || ||||||||||||||||| || || || |||||||| | |||||||| |||
-------------------gtcaaagtgtgtgtat------atatgtctc---ttctccatcctttct--ttagatttcaaaggtaaaaattaggttataatgctagaatgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTCMapped 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|4260267|gb|AI416763.1|AI416763EST: CTAGTGGCCACAGATGTTGCTGCTCGGGGACTGGATATCAAGGACATTAT GGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAG
genomic: CTAGTGGCCACAGATGTTGCTGCTCGGGGACTGGATATCAAGGACATTAGgttgttaatt ... tattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagtcttggaaaagtaaccattgtattttacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
aagtaac putative branch site (score: 2)
attgtattttacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA