Sequence
atgc intronic sequence ATGC exonic sequence...ttatgataatttttttcttggtttattattccatttgtaatattttcttttactttttgacacatctatttggcttggccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
Basic information
species | Glycine max |
transcript | GLYMA10G23680.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 9
--ttatga---taatttttttcttggtttattattccatttgtaatattttcttttactttttgacacatctatttggcttggccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
||| | ||| | | | | ||||| | | ||||| || | | || | ||| | ||| | |||||| | | ||||| |||||||| ||||||||||| | ||||| |||||||| | ||| ||||||||||||| ||||||| ||||| ||||| ||| | || |||| |
aattaagtaattaacgtgatatctatcctcttatttctcatataataatta-tggaaagttcagcaacaaatcgttgattg----attaacgtccaattctgcagATTAATGACCGGTATGAGTTCCCACTTCAACTTGATCTTGACAGAGATGATGGGAAATATCTTGCTCCTGATGCAGATAGAAGCATTAGAAACCTTTACA
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 9
ttatgataatttttttcttggtttattattccatttgtaatattttctttt----actttttgacacatctatttggcttggccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
| | | ||| || | ||| |||| ||| | | ||||| || || || | ||| ||| | |||| |||||||||||||||||||| || ||| |||||||||| | |||| |||| ||||| || ||||| || || ||||| || | || || | ||||
gctcaactgtatcttttacttttgagggaaacatgcaaaatactttatacacacaattttttcctgcactggttaaactaaac---taatttggacaatgt-agATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGATGGAAAATACCTCTCTCCAGAAGCTGACAGGAGGGTGCGTAACCTCTATA
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 5
ttatgataatttttttcttggtttattattccatttgtaatattttc---ttttactttttgacacatctatttggcttg--gccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
| | | |||| | | | | || |||| ||| ||||| || | | || || || || |||| || | ||||| |||||||||||||| ||||| |||||||| ||| | |||| ||| |||| |||||||| |||| || ||||| |||||||| | || |||||
---agccgactagcctctttaatatctctgctgttca-aatactttaaaggtttacgttccggttctgagcttgggatttctgctattatgcctatctgtg-cagATTAATGACCGCTATGAATTCCCTTTGCAACTTGATTTGGATAGAGATGATGGAAAATATCTTGCTCCAGATGCAGATAGAAGTATAAGAAACCTTTATG
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 9
-------ttatgat-aatttttttcttggtttattattccatttgtaatattttcttttactttttgacacatctattt-ggcttggccattaacttgattgg--catcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
|| | ||| | | || ||| || | | | | | | | | || || |||| || | ||| | | ||||| |||||||||||||||||||| | ||||| |||||||||| || ||||| |||||||||||||| || ||||| |||||||| | || | ||||
gttagaaccgtgctgaataccaccatccaaatgataaaccacttccatacatcttaagaaatggtgaataaggttacccaggattggtgatgatcttatctacttctgcagATTAATGACCGCTATGAGTTCCCTCTTCAACTTGATCTTGATAGAGACAATGGAAAATATCTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATA
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 5
-----ttatgataatttttttcttggtttattattccatttgtaatattttcttttactttttgacacatctatttggcttggccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
| | || || | | || || | | | | | || | || | | || | ||| | | || || || | |||| |||||||| ||||||||||| | ||| | |||||||||| ||| |||| |||||||| ||||| ||||| || |||||| | || || | ||||
ggatatcactatcatctgagacatgcattcaaaatacttgtctatggctgatttgcattctt----gcgtcttctaaattaaattgtttttttttgtgatgt-agATAAATGACCGTTATGAGTTCCCACTTCAATTGGATCTTGATAGAGATGATGGAAAATATCTTTCTCCAGACGCGGATAGAAGTGTGCGTAACCTATATA
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
--ttatga-taatttttttcttggttt--attattccatttgtaatattttcttttactttttgacacatctatttggcttggccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
|| ||| ||| ||| | || || | | || | | | | | ||| | || | | || | | | || || | | || ||||| |||||||||||||||||||| |||||||| |||||||||| || ||||| ||||||||||| || || || || || ||| |||||||| |||| |
ccttgtgactaaggtttcttttatttctgagaaatcaaacacgtgtgtgtgcctttgtctgttaata-----gctttgataaactgttccactggtggccaacagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------------------------------------------ttatgataatttttttcttggtttat-tattccatttgtaatattttctt-----ttactttttgacacatctatttggcttggccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
| | | | | | | | || | | |||| ||||| | || || | ||||||| || | ||| ||| ||||| || || | ||||| ||||| ||||||||||| || |||||||||| || |||| || ||||| |||||||| |||||||| || ||| | ||| | || ||||| || |
gtgaggaaaggggttttcgaaccatgcaatatgcaacattcggctggtatagcttatgtattgattgtgcatattatttagatgaaggacgtgtgtgtgtgtgtgtgtgtatttgctttgttttggttggttggtagtcacttttttac-tactgattacctttgaacatta--tttatgtgatgcagATTAATGATCGCTATGAGTTTCCTCTGCAACTAGACCTGGATAGAGAGAATGGAAAATATCTCTCTCCTGATGCTGACCGCAGTGTGCGAAATTTATACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttactttttgacacatctatttggcttggccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
tacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgataatttttttcttggtttattattccatttgtaatattttcttttactttttgacacatctatttggcttggccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - ccatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattaa