Sequence
atgc intronic sequence ATGC exonic sequence...cttgtccaagcatcctagtctgctttaatttttgaaacaaaagaaatatgctttaaggattagtgtaggatgattctaacttaacagaggtgtaatgcagATGGTTAGGATGTTAGATATACTGGGAGAGTATATGTCCCTTCGAGGGTTTCAATTTCAGAGGCTTGATGGCAGTACAAAAGCTGAGCTTCGACAACAAG
Basic information
species | Glycine max |
transcript | GLYMA14G03780.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 7
-cttgtccaagcatccta-gtctgctttaatttttgaaaca-aaagaaatatgctttaaggattagtgtaggatgattctaacttaacagaggtgtaatgcagATGGTTAGGATGTTAGATATACTGGGAGAGTATATGTCCCTTCGAGGGTTTCAATTTCAGAGGCTTGATGGCAGTACAAAAGCTGAGCTTCGACAACAAG
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caacatcaatatatcggacaacgaatatattatatgtcgcttgaaagcatttgcaccttagataact-tatataagtgctttctgaatcaaattgt--tgcagATGGTTAGGATGTTGGACATCCTTGCTGAGTATCTATCCCTCCGAGGATTCCAGTTTCAGAGGCTTGATGGCAGTACGAGAGCAGATCTTCGTCACCAGG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 17
--cttgtccaagcatcctagt-ctgctttaatttttgaaacaaaagaaatatgctttaagg-attagtgtaggatgattctaacttaacagaggtgtaatgcagATGGTTAGGATGTTAGATATACTGGGAGAGTATATGTCCCTTCGAGGGTTTCAATTTCAGAGGCTTGATGGCAGTACAAAAGCTGAGCTTCGACAACAAG
|| || ||| ||| || | || ||| | || |||||| ||||||| || | | ||| | ||| | || | |||||||||||| |||||| || || || | ||| ||| | |||||||| || ||||| ||||||||||||||||| ||||||| ||| || ||||| || ||||
taggagttaaaacattacagtgctcacatgatatttctga-aagcaaaatattttttaaggtatctgcgcctaatgtggattact-acttgacacct--tgcagATGGTTAAGATGTTGGACATCCTTGCAGAATATCTCTCCCTTCGGGGATTTCAGTTTCAGAGGCTTGATGGTAGTACAAGAGCAGATCTTCGTCATCAAG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 21
cttgtccaagcatcctagtctgctttaatt--tttgaaacaaaagaaa-tatgctttaagg-attagtgtaggatgattctaacttaacagaggtgtaatgcagATGGTTAGGATGTTAGATATACTGGGAGAGTATATGTCCCTTCGAGGGTTTCAATTTCAGAGGCTTGATGGCAGTACAAAAGCTGAGCTTCGACAACAAG
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catacctattt-tcttattgtgctatcatcaatatgttggaaagaaaactattttttaaagcatctgcgcctcaggtggtttacttcat---gattccttgcagATGGTTAAGATGTTGGACATCCTTGCAGAATACCTCTCTCTTCGGGGATTTCAGTTTCAGAGGCTTGATGGTAGTACAAGAGCAGATCTTCGTCATCAAG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 18
cttgtccaagcatcc--tagtctgctttaatttttgaaacaaaagaaatatgctttaagg-attagtgtaggatgattctaacttaacagag-gtgtaatgcagATGGTTAGGATGTTAGATATACTGGGAGAGTATATGTCCCTTCGAGGGTTTCAATTTCAGAGGCTTGATGGCAGTACAAAAGCTGAGCTTCGACAACAAG
| | | || | || ||| | || |||||| | | | || | | | |||| | ||| | | ||| || | |||||||||||||| ||||| |||||||||| ||| |||||||| ||| ||||||| ||||||||| |||||||||| |||||||| |||||| | || || || |
--agattagtcgtctattgatcaaaattatgtctt--aacaaactatctttatttagggatacaattgtactggctatttaagtgacaagattgttttatgcagATGGTTAGAATGTTGGATATACTGGCAGAATATATGTCACTTAGAGGGTTCCAATTTCAGCGGCTTGATGGTAGTACAAAGGCTGAGTTGCGTCAGCAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgctttaaggattagtgtaggatgattctaacttaacagaggtgtaatgcagATGGTTAGGATGTTAGATATACTGGGAGAGTATATGTCCCTTCGAGGGTTTCAATTTCAGAGGCTTGATGGCAGTACAAAAGCTGAGCTTCGACAACAAG
taacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgtccaagcatcctagtctgctttaatttttgaaacaaaagaaatatgctttaaggattagtgtaggatgattctaacttaacagaggtgtaatgcagATGGTTAGGATGTTAGATATACTGGGAGAGTATATGTCCCTTCGAGGGTTTCAATTTCAGAGGCTTGATGGCAGTACAAAAGCTGAGCTTCGACAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - caagcat
- - - - - - - - agtctgc
- - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - tatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtagg