Sequence
atgc intronic sequence ATGC exonic sequence...acttttgatagttatcatttgttttagtcctgatcctgatataagtctctgcaatcctttccatgaatttattttgagtttgtcagtaatacatgtgcagAGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTAGTTTGAAAGATAGTGTTGAGAAAGACACCTTCTTCCGCAAGCTTCCAAA
Basic information
species | Glycine max |
transcript | GLYMA20G36180.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G098078_T02 (Zea mays), 3'ss of exon 8
----------------------------------acttttg-----atagttatcat-ttgttttagtcctgatcctgatataagtctctgcaatcctttcca----tgaatttattt------------tgagtttgtcagtaatacatgtgcagAGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTAGTTTGAAAGATAGTGTTGAGAAAGACACCTTCTTCCGCAAGCTTCCAAA
||||||| | | |||||| || || ||| | | || || | | || ||| | || |||| || || | | | | | | |||||| ||| || |||||||| ||||| || || || |||||||||||||||| ||||||||| | |||||||||||| ||| ||||| |||||||| ||
gtaagctcaacatatttttcatgtcgttcagtcaacttttggggtgacatttatcacatttcttcagtgcatagtcttatcacaattattgtcctccatgtgggaattgcatttgttcgaaaagctgaaatggtgtctttggctctctgttttcagAGTTTTTCCAGAATAAGTTAGTAGAGACTATCCAGTTCATGGAAATTCTTAATTTGAAAGACACCTTTGAGAAAGACAGCTTTTTCCGGAAGCTTCCCAA
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 8
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 8
------------------------------------------------acttttgatagttatcat---ttgttttagtcctgatcctgatataagtctctgcaatcctttcca----tgaatttattttgagtttgtcagtaatacatgtg-----------cagAGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTAGTTTGAAAGATAGTGTTGAGAAAGACACCTTCTTCCGCAAGCTTCCAAA
| ||| || |||| || || || | | || | || | | | || ||| | || |||| || | | | | | || |||||| ||| || || ||||| ||||| || || || |||||||||||||||| ||||||||| | |||||||||||| || || || || || || ||
gtaagctcaacatattttctgtgtcgttcagccaacttttggggtgtcattttatctaattataatacatttcttcaatgcttagtcttaccacaattattgtcctccatgtgggaattgcatttgttcaaaaagctgaaatggtgtctttggctctctgtttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATCCAGTTCATGGAAATTCTTAATTTGAAAGACACCTTTGAGAAAGACAGTTTTTTTCGTAAACTCCCCAA
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 8
acttttgatagttatcatttgttttagtcctgatcctgatataagtctctgcaatcctt-tccatgaatttattttgagtttgtcagtaat-acatgtgcagAGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTAGTTTGAAAGATAGTGTTGAGAAAGACACCTTCTTCCGCAAGCTTCCAAA
| ||| | | | || | | | | || ||| | ||| | | || | || || ||| | | ||| || | || ||||||||||| ||||||||| |||| ||||| |||||||| ||||| ||||| | |||||||| ||||| || ||||| || ||||||||||| ||||||||
-gtcttggtt-tctttatataacgtgttgtattttctctcatagttatctttgaccattctttatctcttgattcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 8
acttttgatagttatcatttgttttagtcctgatcctgatataagtctctgcaatcctttccatgaatttattttgagtttgtcagtaatacatgtgcagAGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTAGTTTGAAAGATAGTGTTGAGAAAGACACCTTCTTCCGCAAGCTTCCAAA
| || | | | | | | || | | ||| | || | | ||| | | | | | || || || ||| ||||| ||||| ||||||||||| || || || |||||||||||||| ||||||| |||||| || |||||||| || || ||||||||||| |||||||||||
atttctttgcctcagtctctttcttcttagtattcccttctttcttccttttcctttttttttttggtgcctactaatttcagaagatatgcattggcagAATATTTCCAAAATAAGTTAGTGGATACTATACATTTCATGGACATTCTTAATTTGAAGGACAGTGTTGAAAAGGATACCTTCTTCCGTAAGCTTCCAAAMapped 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|37997477|gb|CF809066.1|CF809066EST: TTCTGTGCCCTCTCGTAGATTAAATACATCAAAGCTTATAGAAAACAGTG AGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTA
genomic: TTCTGTGCCCTCTCGTAGATTAAATACATCAAAGCTTATAGAAAACAGTGgtgagtgctt ... acatgtgcagAGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctgcaatcctttccatgaatttattttgagtttgtcagtaatacatgtgcagAGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTAGTTTGAAAGATAGTGTTGAGAAAGACACCTTCTTCCGCAAGCTTCCAAA
aatttattttgagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttttgatagttatcatttgttttagtcctgatcctgatataagtctctgcaatcctttccatgaatttattttgagtttgtcagtaatacatgtgcagAGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTAGTTTGAAAGATAGTGTTGAGAAAGACACCTTCTTCCGCAAGCTTCCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - -ctgatcc
- - - - - - - - - - - - - - - - - - - - - - - ctctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagtttg