Sequence
atgc intronic sequence ATGC exonic sequence...agctaatgcttaaatgcatgaatttggaagttgtaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttattgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA12G37100.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 14
-----------------------------------------------------------------------------------agctaatgcttaaatgcatgaatttggaagttgtaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttattgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
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gtataatgatgcgctgatgcaccataggttatcattcctgtagtttttttttatttactctggctcttcacagctagtgtaatctttcatttgtagttacaagtaactgcagatggttttggttaattctgtatcctggtttggcttttttgcatataagatgatttcttcttttctactcagGCTACCTTTTGAAGAAAAGTGCAAAAAATAATGAATGGAGCAAAAGATGGTTTGTCCTAAATGAGAAGAGTGGAAAG
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
agctaatgcttaaatgcatgaatttgga-agttgtaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttattgtt-tgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
| || | | |||| | | | |||| ||| || ||| | | | | | || |||| || |||| | ||| || | |||| | | || ||||||||||||||||| ||||| ||||| ||| | |||||||| || |||||||| | ||||||
-ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaata-taaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 14
-agctaatgcttaaatg--catgaatttggaagttgtaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttattgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
| ||||| || || || || | ||| | || | | || | | |||| | | ||| || | |||| | | | |||||| | | ||||||||||| |||||||||||||| ||||||| |||||||||| || |||||||||| ||||||
gatgagctgcttcaaccactttgcatgtgttcatggtagcgatacattttgattgatttgagaa-gttaacata-taagcatattcttctgt-tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G485898_T02 (Zea mays), 3'ss of exon 14
-------------------------------------------------------------------------------------agctaatgcttaaatgcatgaatttggaagttgta-atgtgccaaagta---tatatttcaaaattatt-----aataaacta-aaactacttttctttattgtttgc---agGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
|| | || || || || || ||| || | || | | | ||| || | || || || || | | | | | | || ||||| ||| |||||||| || ||| | |||||| | |||| |||||||| |||||||||||| ||||||||||| | ||||||
gtattaccctactgcaatttggtttttgaatgaaagaccctactacaattattgtatatttaccatcatcaaacttattaggtaaagatcataactagtaaaatagatggaagagctgtccataaacagaactgttttgtgtttttaatcttttccttggattaattacatagtgagtgcatgttttctttgctaaagGTTTTTTGTTCAAAAAACGCGCAAAAGCAAATGATTGGAGCAAGCGATGGTTTGTTCTAAATGAGAAAAGTGGAAAG
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 2
agctaatgcttaaatgcatgaatttggaagttgtaatgtgccaaagtatatatttcaaaattattaataaac-taaaactacttttctttattgtt-tgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
| | | || | | | || ||| | | ||| | | | | | | ||||| || || || || | | || | |||||| | | ||||||||||| |||||||||||||| ||||| | | |||||||| || |||||||||| ||||||
-gttgtatttcaactctagcctgtcctaacttgcttgggactaaaaggctt-tgttgttgtgagaagtaaacctataattatattcttctgttcctatgcagGTTACCTCTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGTAAAAGGTGGTTTGTTCTTAATGAGAAGAGTGGAAAG
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 14
----agctaatgcttaaat--gcatgaatttg-gaagttgtaatgtgcca-aagtatatatttcaaaattattaataaactaaaactacttttctttattgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
|||| | || | || | ||| || ||| || | || | || | | | | || | || | || ||| | || | | |||| ||||| | || | |||||||||||||| || ||||| ||||| |||||||||||||| || ||||| || || ||||||
ctttagctttgacctagcgtaggataagtttttgaggttttagtttgttataaaaaccaactgccaaggtcttca---acagaaatt---ttattctgttgt--gcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 14
agctaatgcttaaatgcatgaatttggaagttgtaatgtgccaaagtatatatttcaaaattatt------aataaactaaaactacttttctttattgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
||| || | |||| ||| | || ||| || | | ||||| || || | | || ||||| || | ||| ||| | || | ||||||||||||||||| ||||| ||||| |||||||||||||| || |||||||| || ||||||
--tgcatgatttc-ttcatgtctttttcttctttatcacttaaaacta-acttgacaaaactaacttccaaggtagataacaaatacttactcttttcattt--agGGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAG
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 14
agctaatgcttaaatgcatgaatt-tggaagttgtaatgtgccaaagtatatatttcaaaattattaataaactaaaact-----actttt--ctttat-tgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
||| ||||| ||| || | || | ||| ||| | | | | || | | || || || ||| |||||| | | |||| ||| | || |||||||||| |||||||||||| |||||||||||||||||||| ||||||| ||||| || |||
---------ataatggcatgtattgtgcatcttctcttgtatcaacatctctctctctctctctctctctctctctctctctccaaccttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatatatttcaaaattattaataaactaaaactacttttctttattgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
aactaaa putative branch site (score: 2)
cttttctttattgttt putative PPT
tatttcaaaattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agctaatgcttaaatgcatgaatttggaagttgtaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttattgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
-gctaatg
- - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - tgccaaa