Sequence
atgc intronic sequence ATGC exonic sequencegtataatgatgtattaaatcattattcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA
Basic information
species | Glycine max |
transcript | GLYMA17G14820.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 8
gtataatgatgtattaaatcattattcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA
| |||| | | | ||| | || || || ||||| | || || | || ||||||| | |||| ||||||||||||||| |||||||| || || || ||||| ||||| ||||||||||||||||| ||||| |||||||| || ||| | |||| |
----------------------------gtatgcgcaaagcatataattcgcct--attgttagttttttgtagt-gcaaagcctaa---cgtactatttgatgatttgttaa-gGAGAAGCTTCCACCAACGGATTCAAGACTCAGGCCAGATCAGCGGCATCTAGAGAATGGGGAGTACGAAAAGGCTAACTCTGAAAAATTGCGCCTGGAGA
upper sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os08g05870.1 (Oryza sativa), 3'ss of exon 7
gtataatgatgtattaaatcatta-ttcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA
|||| | | |||| | | | | ||| || | | ||| ||| || || | || || || | | ||| ||| | | |||||| || || || || || ||||| |||| || ||||||||||| ||||||||||| || ||||| |||||||| || |||||| | |||||||||
------gtatgtgtgtagtcatgaatactccacaagctttgaattgtttacttg-atatc---aagactcaatgat-------cctaatt--gaattgattggtcatgt-tcaaagGACAAACTCCCTCCTACTGATTCACGGCTAAGGCCAGACCAGCGGCATCTAGAGAACGGTGAATATGAGAAGGCAAACGCGGAGAAGCTGAGGTTGGAAC
upper sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
gtata-atgatgtattaaatcattattcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA
||| | ||| || || || | | | | |||| || |||||| | || |||| || | | | ||||| | |||| | ||||||||||| ||||| |||||||| |||||||||||||| || || || || ||||||||||| ||||||||||| ||| || |||| | | || |
gtacacatggaacataaa--tataacccatcattggacttccgttag-ttctta---acctataatgctaaggcaca----tttctaccct-------tttgtt---------aagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
upper sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G402653_T05 (Zea mays), 3'ss of exon 3
gtataatgatgtattaaatcattattcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA
| || | | | | | || | | | || | || || ||| | | | || ||||| | |||||| |||||||| || ||||| ||||||||||||||||||| || ||||||||||| ||||||||||| || ||| ||||| | |||||||||
----------------------------gtatggatctacatgtggattgccacataaaagtgtttggtaacta-agtttttgtccttaattgcttggccattcctggattca-gGAGAAACTTCCACCTACTGATTCACGGCTGAGACCAGACCAGCGCCACCTAGAGAATGGTGAATACGAGAAAGCGAATGCAGAGAAGCTGAGGTTGGAAC
upper sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
gtataatgatgtattaaatcattattcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA
|| ||| | | | ||| | || | | || || ||||| | || || || | | | ||||| | || | | ||||||||||| ||||| |||||||| |||||||||||||| || || || || ||||||||||| ||||||||||| ||| || |||| | | || |
--gtacacatggaacatacatatatcccataatctgagttctgttagctctta---acctaaaaggctacgacaca-tcttttacgctcttg------------------ttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
upper sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 7
gtata-atgatgtattaaatca-ttattcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA
||| | || ||||||| ||||| || || |||||| | ||| |||| | |||||||||| ||||||| | | ||||||| | |||||||||||||| |||||||||||||||| ||||||||| |||||||||||||| || || |||||||| || ||||||||||||||||| ||||| || ||||| ||| || |||| | |||| || |
gtagagataatgtattgaatcaatttttttatgtgcatattcatttt-cctcttatgcatatctaattgtcttttatagctctgtctgatcccgggta-tttgatcacggattaa-gGAGAAGCTCCCACCCACGGATTCAAGACTTAGACCAGATCAACGACATCTAGAGAATGGAGAATATGAAAAGGCAAATGCAGAAAAACTACGGTTAGAGAMapped 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|6746936|gb|AW317392.1|AW317392EST: ATTTGACATCATTTGCCATCACACTGAATGAGCTTACTCCCGGGCTAAAG GAGAAGCTTCCACCCACCGATTCCAGGCTGAGACCAGACCAGCGACATCTA
genomic: ATTTGACATCATTTGCCATCACACTGAATGAGCTTACTCCCGGGCTAAAGgtataatgat ... cggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA
tttgttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatgatgtattaaatcattattcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA