Sequence
atgc intronic sequence ATGC exonic sequence...agtgaatggagaacaataggagcttgttgaaatactaaagtatcagtagatcttatggtatgatatatcttataatcataatattcttggactggagcagTGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGTTTACAGTGATTCAAGCCAAGTTG
Basic information
species | Glycine max |
transcript | GLYMA20G16030.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G16030.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0041g00100.t01 (Vitis vinifera), 3'ss of exon 12
agtgaatgga-gaacaataggagcttgttgaaatactaaagtatcagtagat-cttatggtatgatatatcttataatcataatattcttggactg-gagcagTGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGTTTACAGTGATTCAAGCCAAGTTG
|| || | ||||| | || ||| ||| | | ||| || | | || ||| | || | | || || |||| || | |||||||||| || |||||||| ||||| |||||||| ||||||||||||||||| || || ||| |||||||| | |
--tgcttgcacaaacaacaccag-ttggagaagtgtttttctatttttatttgcacctgcaatggtttactactcagtaatcattgacttgccttgcgtgcagTGCAGGGATCACTGAAGGCTTTTCAATGTGTGGTGGTGACTTTGTTGAAGTCTATAGCGATCCAAGCCAAATAG
upper sequence: GLYMA20G16030.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S249_29V6.1 (Physcomitrella patens), 3'ss of exon 12
agtgaatggagaacaataggagcttgttgaaatactaaagtatcagtagatcttatggtatgatatatcttataatcataatattcttggac--tggagcagTGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGTTTACAGTGATTCAAGCCAAGTTG
| || | | | || |||| | ||| | | | | || | | | | || || ||| | | || ||||||||||||||||| | |||||||||||||||| || || ||||| || || || ||| || || |||| | |
-ggatctgcatcgtcctgctaagtttctgaact-ctagtatcttacaacattactttagcttttcttctgagcaaatatcttatggtaaaataatgaagcagTGCAGGAATTACAAACGGTTTTTCCATGTGTGCTGGGGATTTTGTGGAGGTCTATAGTCATCCAGGCCAGGCAG
upper sequence: GLYMA20G16030.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ35517 (Selaginella moellendorffii), 3'ss of exon 5
agtgaatggagaacaataggagcttgttgaaatactaaagtatcagtagatcttatggtatgatatatcttataatcataatattcttggactggagcagTGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGTTTACAGTGATTCAAGCCAAGTTG
| | ||| ||| || || || | | || || |||| | || | ||||||||||||||||||||| ||||| ||||||| ||||| ||| | || ||||| | | |||||| |
-------------------------------gttttctagttccagcag---cgatcttacagttcagctcatgg-----atatcc--agat---aacagTGCAGGAATTACTGAAGGCTTTTCGATGTGTGCCGGTGATTTTCTGGAGGTTTATGGCCACGAGAGCCAAACAG
upper sequence: GLYMA20G16030.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ24256 (Selaginella moellendorffii), 3'ss of exon 5
agtgaatggagaacaataggagcttgttgaaatactaaagtatcagtagatcttatggtatgatatatcttataatcataatattcttggactggagcagTGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGTTTACAGTGATTCAAGCCAAGTTG
| | ||| ||| || || || | | || || |||||| || | ||||||||||||||||||||| ||||| ||||||| ||||| ||| | || ||||| | | |||||| |
-------------------------------gttttctagttccagcag---cgatcttacagttcagctcatgg-----atattc--agat---aacagTGCAGGAATTACTGAAGGCTTTTCGATGTGTGCCGGTGATTTTCTGGAGGTTTATGGCCACGAGAGCCAAACAGMapped 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|7685675|gb|AW756323.1|AW756323EST: GACAGTGATCAACTTCGTCCTGTTTCAATACCAGATATGCATCCAGCCAG TGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGT
genomic: GACAGTGATCAACTTCGTCCTGTTTCAATACCAGATATGCATCCAGCCAGgtatatacat ... actggagcagTGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGT
EST:
gi|308098770|gb|HO760511.1|HO760511EST: GACAGTGATCAACTTCGTCCTGTTTCAATACCAGATATGCATCCAGCCAG TGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGT
genomic: GACAGTGATCAACTTCGTCCTGTTTCAATACCAGATATGCATCCAGCCAGgtatatacat ... actggagcagTGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagatcttatggtatgatatatcttataatcataatattcttggactggagcagTGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGTTTACAGTGATTCAAGCCAAGTTG
tatgatatatcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgaatggagaacaataggagcttgttgaaatactaaagtatcagtagatcttatggtatgatatatcttataatcataatattcttggactggagcagTGCAGGAATTACTGAAGGTTTTTCCATGTGTGGAGGTGACTTTGTTGAAGTTTACAGTGATTCAAGCCAAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- tgaatgg
- - - - - - - - - - -gcttgtt
- - - - - - - - - - - - - - gaaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtatga