Sequence
atgc intronic sequence ATGC exonic sequence...tttgtgttttgcatattatatatatataccaattccccacacttgatttgtggagaatttttacacggtgttaactaattgatgtcttataacttttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
Basic information
species | Glycine max |
transcript | GLYMA02G14110.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G14110.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
tttgtgttttgcatattatatatatataccaattccccacacttgatttgtggagaatttttacacggtgttaactaattgatgtc-ttataacttttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
| | ||| | | |||||| | || | ||||| | ||| | ||||| ||||| | ||| || | ||| |||| |||||||| ||||| || ||| ||||||||||||| ||||| ||||| |||||||| || |||||||| || | ||||| |||||||| || ||||
-agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
upper sequence: GLYMA02G14110.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
tttgtgttttgcatattatatatatataccaattccccacacttgat-ttgtggagaatttttacacggtgttaactaattgatgtc-ttataacttttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
|| ||| | | | | | || | | || ||| | | | ||||| | || | || | || ||||||||||||| || || | ||| ||||||||||||| || |||||||| |||||||| || ||||||||||| | ||||| |||||||| || ||||
-ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctggcagccctggtgtt-cactaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
upper sequence: GLYMA02G14110.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G26190.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------tttgtgttttgcatattatatatatataccaattccccacactt--gatttgtggagaatttttacacggtgttaactaattgatgtctta---taacttttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
| | || |||| |||| | | | | | | | | |||| | | || ||| || | | ||| || || | | ||||||||||| || |||| || ||||||||||| ||||| ||||| ||||| |||||||| ||||| |||||||| || ||||| ||||||||||||||||
gtttgttcagagtttattttccatgttctcatcaatatgactattcaatatctggaaaagctgacaatccctctgattctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
upper sequence: GLYMA02G14110.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0010g01080.t01 (Vitis vinifera), 3'ss of exon 5
tttgtgttttgcatattatatatatataccaattccccacacttgattt-gtggagaatttttacacggtg-ttaactaat-tgatgtcttataact--tttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
||| | || | | | | || | || | | ||| || | | ||| || || | ||| |||| || || |||||||||||||| || ||||| |||||||| |||||||||||||| |||||||| ||||||||||| ||||||||||| |||||||| ||||| ||||||||||
---acaccttgtct-ttgtctg-gtttgttaacttcctaaggtcattttagtccatgagaaatacgcgagacttgcccaatctgatcagttggttctcatttcagGAATGGGTTACTGATAATCCATTTGTTATATCACCAAGAATAACTTTTGAAGTCAGTGTGCGGCTTCTTGGTGGGCTAATGGCCTTGGGGTACACAATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtggagaatttttacacggtgttaactaattgatgtcttataacttttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
ttataac putative branch site (score: 2)
cttttc CT-rich tract
ttataactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtgttttgcatattatatatatataccaattccccacacttgatttgtggagaatttttacacggtgttaactaattgatgtcttataacttttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
tttgtgt
- - - - -tgcatat
- - - - - - - - - - - - - - - - ttcccca
- - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtc