Sequence
atgc intronic sequence ATGC exonic sequencegtatgcctctttttccttaaaacatagttgatcctcatttagtgtcgatgtatttagtattttagttatgtacaccctgcaagaggctttcagttcatgttatgcattaaaattgaccatttaactattaagcatatcacttcataatgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATTAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
Basic information
species | Glycine max |
transcript | GLYMA05G36070.2 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G36070.2 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 5
gtatgcctctttttccttaaaacatagttgatcct---------catttagtgtcgatgtatttagtattttagttatgtacacc-----ctgcaagaggctttcagttcatgttatgcattaaaattgaccattta--actattaagcata--------------------------tcacttcataatgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATTAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
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gtatgtgtgcttcttcacaaatcacaagtgaatctagatatattcaattggatccaacctttgtggtccttttcttgtaccacccttaagctccgagactcttttgagccaactaaccatttaaatctgcctgtagggtactatcagaaatacttcaaatggtgttctaattttgctttctcttcgtttt-cagATATGAAGATGCATTTAATAGATTTGTCGATGAGATAAACACCCTTGCAGCTTATCAATGGTGGGAAGGATCTATTTACAGTATCCTCTGTATACTTGCC
upper sequence: GLYMA05G36070.2 (Glycine max), 3'ss of exon 16
lower sequence: PP1S164_9V6.1 (Physcomitrella patens), 3'ss of exon 15
gtatgcctctttttccttaaaacatagttgatcctcatttagtgtcgatgtatttagtattttagttatgtacaccctgcaagaggctttcagttcatgttatgcattaaaattgaccatttaactattaagcatatcacttcataatgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATTAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
|| | | ||| | ||| | || | | | | | | || | | | || | | | | ||| | | | | | |||||||||||| ||||| || || || |||||||| ||| | ||||| ||||| | ||||| |||||||||||||| | | |||||||| || ||||
-----------------------------------------atgctctcctctgctgtaaatcagtaacgtctattttatgaaa---------cttcttttgtaactcgtagttctttact--agtcttatgatcaaccttcttttatgcagATATGAGGATGCTTTTAACAGGTTTGTGGAGGACGTCAATAGCTTAGCAGCATATCAATGGTGGGAAGGGTCCGTGCATAGTATCCTGATAATGCTTGCC
upper sequence: GLYMA05G36070.2 (Glycine max), 3'ss of exon 16
lower sequence: PP1S258_17V6.1 (Physcomitrella patens), 3'ss of exon 11
gtatgcctctttttccttaaaacatagttgatcctcatttagtgtcgatgtatttagtattttagttatgtacaccctgcaagaggctttcagttcatgttatgcattaaaattgaccatttaactattaagcatatcacttcataatgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATTAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA-
||| || | | |||| | ||| | ||| |||| || || | ||||| | | || | ||| ||| || ||||| || | | | || || | | | |||||||||| ||||||||||| || ||||||||||| | ||| | || || | ||||| |||||||| || || | ||||||| || || |||
----------------gtaagtcacacattcccctc-tacagttttgat-tattcag-gttgggatgatgtaga---tataaaaa---ttctcttcctgc---------aaatt-----ttcatatgtgaaaaatgtggccc---acggcagATATGAGGATGCCTTCAACAGGTTTGTGGATGAGGTGAATGGCTTGGCAGCGTATCAATGGTGGGAGGGCTCAGTGCACAGTATT-TTAACACTATTAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttatgcattaaaattgaccatttaactattaagcatatcacttcataatgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATTAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
atttaac putative branch site (score: 3)
tcacttc putative PPT
atttaactattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcctctttttccttaaaacatagttgatcctcatttagtgtcgatgtatttagtattttagttatgtacaccctgcaagaggctttcagttcatgttatgcattaaaattgaccatttaactattaagcatatcacttcataatgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATTAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG