Sequence
atgc intronic sequence ATGC exonic sequence...taacttttgttagaagtagctccatgctgcatcctaacccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
Basic information
species | Glycine max |
transcript | GLYMA06G14980.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g60780.2 (Oryza sativa), 3'ss of exon 1
--taacttt--tgttagaagtagctccatgctgcatcctaacccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
| | | | | | | | ||| | | | ||| || | | | | | | || |||| | | ||||||| || ||||||| |||||||| || || ||||||||||||||||||||||| || || ||| ||||| ||| ||||| ||| || | || |
tatgagtacaatatgacgaacaataccacctgagaaaactaactgtttcctaagctatataaccatgcaaaaatcacagcac---tctcctaatttcttt-cagCTACTACGCTGACAAGCTGGCATCTCCTGGTGACATTTTGTTCCCTTCATGTGGCTCTTCAGATGAAGCTTTTCGAGAACAAAGATTTAGACCCCAAGAC
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 2
taacttttgttagaagtagctccatgctgcatcct------aacccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
||||| | | | | | | ||| | | || | |||| |||| | | | ||| ||| | ||| ||| |||||| || || ||||| ||||||||||||||||| |||||||| ||||| ||||| ||| || | ||| | || |||||||| ||||| || || | |
-ttcttttctcaaatgcattgcaatgtattagtgtttgtagaatttacatgaatataaatgacaccaact--gtttttccatacatggaattgtattt---tgcagCCACTACCTTGACGAGTTGGCATCTTCTTGTCACATTTTGCTCCCTCCATGTAGCATTATGGATGAAGTTCTTCGAGCACAAGCCTTTCGACTCGAGAAC
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
taacttttgttagaagtagctccatgctgcatcctaacccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcc--catgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
|| | || | | | | | ||| || | | ||| | | | | | || | | | | | |||||| || ||||||||||| |||||||| || || |||||||| || ||||| |||||| || ||| || |||||||||||||||||||| | |
--ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 2
taacttttgttagaagtagctccatgctgcatcctaac--ccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
|| | | || || | | | | || | | | || || | | | | || |||||| || | | |||||| || ||||||||||| |||||||| || || ||||| ||||| || ||||||||| || ||| || ||||||||||||||||| || | |
caagtgtggtgaggtgacagtgcgt-ctataaacagataatgatagcaaagaaggcaggttttcctccaagtgttaataaa-atgtggtattcattttgcagCCACTACTTTGACAAGCTGGCATCTCCTGGTTACATTCTGTTCTCTCCATGTGGCATTATGTATGAAGCTGTTTGAGCACAAACCTTTCGATGCAAGGAC
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 2
-----taacttttgttagaagtagctccatgctgcatcctaacccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
||| | ||| | | | || | || | | | || || | | | | | || | |||| | | || | | ||| ||| |||||| || || |||||||| |||||||| || || ||||| || ||||||||||||||| || | ||| | | |||||||| || |||||||| | | |
acacgccccttattttatcaacatgtg-gtggagtatgcaagtctgatttaaatgtcttcttatgga-ctatggttgtgaaatatgtatttgtcttc---tgcagCCACTACCTTGACAAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTGGCATTATGGATGAAATTCTTTGAGCATAAGCCTTTTGATTCAAGAAC
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
taacttttgttagaagt-agctccatgctgcatcctaacccatt--tgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
||| | || | |||||| | || | || || | | | || ||| || | | | | || | | | | | |||| || ||||||||||| ||||||||| | || ||||||||||| |||||||||||| || | ||| ||||||||||||| |||||||| | |||
---tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
taacttttgttagaagtagctccatgctgcatcctaacccatttgaagta----taatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
||||| | || |||| | || ||| | | | | | || || || | ||| | | | | || | | |||| || ||||||||||||||||||||| | || |||||||||||||||||||||||| || | ||| | || || ||||| |||||||| | |||
--cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattttgta--tgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
--taacttttgttagaagtagctccatgctgcatcctaacccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
|| | || | ||| | | || | | || | | | | | | | ||| || ||| | | || | | | ||||||| || |||||||| ||||||||||| || || || ||||| ||||||||||| ||| | ||| | | ||||| |||||||| ||||| |||||
gctattaggcggtaacaa-agcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccg-tctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
ttttaat putative branch site (score: 3)
ttcccat putative PPT
ttttaatatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taacttttgttagaagtagctccatgctgcatcctaacccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - -ccatgct
- - - - - - - - - - - - - - - - -ctaaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgagg