Sequence
atgc intronic sequence ATGC exonic sequence...atcaattactaatggaagttaatggtgtaactgacttgtgattgacagtttttatacttctgatttaatatttttttgttattatattttgttgttgcagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA
Basic information
species | Glycine max |
transcript | GLYMA14G09020.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g28560.1 (Oryza sativa), 3'ss of exon 2
atcaattactaatggaagttaatggtgtaac-tgacttgtgattgacagtttttatacttctgatttaatatttttttgttattatattttgttgttgcagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA
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ctcttctttaagatgtcttttaggttatagccttataggtacctgtaaagttgagtgatgctttttctct-ttactgaagcactctcttttgctgtttcagCGGAAACTTCTGGTACCACTGTTACATTTGTAGTAATAGATGAGTGGGTTGTAACGGTAGCATCAGTTGGTGATTCACGTTGCATACTAGAATCTGCTGA
upper sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g27780.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------------------atcaattactaatggaagttaatggtgtaactgacttgtgattg-acagtttttatacttctgatttaatatttttttgttattatatttt----gttgttgcagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA
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gtattattctttcactaagctgataacgatttagaggatgtgcatgtaatttagaggcttttagttttctttgttcatattctcccccttttggacaaatatctttctgatttatgaatacatgatcagtgttgttatacacttgcactgcggtgtaaactgattgttaccatgttttcagCGGCGCGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCCCGCTGTATCCTAGAATCTGCTGA
upper sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G052699_T02 (Zea mays), 3'ss of exon 2
atcaattactaatggaagttaatggtgtaa---ctgacttgtgat---tgacagtttttatacttctgatttaatatttttttgttattatattttgttgttgcagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA
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-----ctactactagattatactgccatatgttttaccatgtggactatgacgagaaccatctttacgcattactatatcgtatctgttgggttgtctt-ttacagCACGTTCTTCAGGGACAACTGTGACATTTGTCATAATAGATGGATTGGTCATCACTGTTGCATCAGTTGGTGATTCCCGTTGTGTACTACAAGCTGAAGG
upper sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G044382_T01 (Zea mays), 3'ss of exon 2
--atcaattactaatggaagttaatggtgtaactgacttgtgattgacagtttttatacttctgatttaatatttttttgttattatattttgttgttgcagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA
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acatcatgcagcaaaccagtacgagagctgagtccttttgtttttga-accaacaagagatgagatg-agcctcgtttgcctgttccgtgtatatatttcagCTCATTCCTCGGGGACAACCGTGACGCTTGCCATAATTGATGGCTCCGTTGTAACTGTTGCATCTGTTGGTGATTCACGTTGTGTCCTTGAAGCTGAGGG
upper sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------atcaattac-taatggaagtt--aatggtgt-aactgacttgtgattgacagtttttatac--ttctgatttaatatttttttgttattatattttgttgttgcagGCCAAAAA-----TCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA
| | | || |||| || | || |||| |||| | || ||||| ||||| | | | | |||| || |||| | || ||||| || || |||||||| ||||| || |||||||| ||||||||||||| || | |||||||| || ||||| || |||||| ||||||| || ||||
gtatgaacttatcaatgaaaaaccttgtgatgtgattcaagtcccaagagggtgaactcgtctgtgtctttatattcttatatcattctggtgaaggctatgtttgaggttttattgttttcttgcatttcagCAAGGACGTCTGGAACGACTGTAACTTTTGTCATAGTAGAAGGATGGGTGGTGAGTGTTGCATCTGTAGGTGACTCTCGTTGCATACTTGAGCCTGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtttttatacttctgatttaatatttttttgttattatattttgttgttgcagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA
ttttgtt CT-rich tract
tttatacttctgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcaattactaatggaagttaatggtgtaactgacttgtgattgacagtttttatacttctgatttaatatttttttgttattatattttgttgttgcagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA
- - - - ctaatgg
- - - - - - - - - - aatggtg
- - - - - - - - - - - - - - - - -acttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acttctg