Sequence
atgc intronic sequence ATGC exonic sequence...cagttttgaagatttagtgttcaattcaatcatcaattcctatgacttaatttggaaataacttatgaagttgctaagcatgcctgcacttgcttaacagATTGAAGCTACTAGTAGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
Basic information
| species | Glycine max |
| transcript | GLYMA06G07690.1 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G07690.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
----cagttttgaagatttagtgttcaattcaatcatcaattcctatgacttaatttggaaataactt----atgaagttgctaagcatgcctgcacttgcttaacagATTGAAGCTACTAGTAGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
| |||||||| | || || | | | | || ||||| ||| | ||| || ||| | | ||| | || | | | |||| | || | | | | ||||| | |||||||| || || |||||| |||||||| ||||||| ||||| ||||||||||| || || ||
taagtaaatttgaaga---aatgcgtgatgcgag----atcttatagtacttagttttgtgctaaatttgatatggatgtattaactgagg-tgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
upper sequence: GLYMA06G07690.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
cagttttgaagatttagtgttcaattcaatcatcaattcctatgacttaatttggaaataacttatgaagttgctaagcatgcctgcacttgcttaacagATTGAAGCTACTAGTAGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACATT-CATCT----------------------------------
|||| | | | || | | ||||||| | | ||| || || || |||||| |||||||| ||||||| ||||| ||||||||||| || | || |
------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
upper sequence: GLYMA06G07690.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G116952_T07 (Zea mays), 3'ss of exon 2
cagttttgaagattt-agtgttcaattcaatc--atcaattcctatgacttaatttggaaataacttatgaagttgctaagcatgcctgcacttgctta--acagATTGAAGCTACTAGTAGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
| ||||||| || |||| || | || ||| | | | || | ||||| | || || || | | | || | || |||| | | | || | | ||||||| | | ||| || || || |||||| |||||||| ||||||| ||||| ||||||||||| || | |
---tcttgaagaattgagtggtctgatatattgagtcattagttttatctggaaactgaaatgaacattgtggt--ctgaactctgaagtgattacatattacagGCTTAGTGTGCTGGCTTATCACTTCAAGACAGGTGTTGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCGCAGTATT
upper sequence: GLYMA06G07690.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------cagttttgaagatttagtgttcaattcaatcatcaattc----ctatgacttaat-ttggaaataactt--atgaagttgc-taagcatgcctgcacttgcttaa---------cagATTGAAGCTACTAGTAGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
| |||||| ||| || ||| | | || | ||| || | ||| | ||| ||||| || || | ||| | || ||| | | | | | |||| | || | | || |||||||||||||| ||| | |||||||| ||||| | |||||| | || || ||||||||||| |||||||| |||||||||
gtaaacacacatgttcttagatgatctgtttcaactgaaagtttggattttgaattacgttttctctcaaagcttttcttatttttgagaattgagagtttagatgtctcttttgttctaaactttttctttgtgttgaaaatatctgcaatctaattgagtcagtatgattttggtcgttgattttggcttccagACTTAAAGTTATCGTGGAATACTTCAAAATGGCTCTGGATTGCTTCTTTGCGGTGTGGTTTGTGGTAGGTAATGTATGGATATTTGGAGGGCATTCATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttaatttggaaataacttatgaagttgctaagcatgcctgcacttgcttaacagATTGAAGCTACTAGTAGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
aaataac putative branch site (score: 2)
cttgctt putative PPT
aaataacttatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagttttgaagatttagtgttcaattcaatcatcaattcctatgacttaatttggaaataacttatgaagttgctaagcatgcctgcacttgcttaacagATTGAAGCTACTAGTAGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - -caattca
- - - - - - - - - - - - - - - - - - - cctatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcct
