Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaacccatcaagtatataaataagttgagtgattaccaacagattagagtcttgagtcctatacctaaatggtgtgttgtgtgatgcagTGTATGCCAAATTGCTATGCAAGGATTATGAGTGTAGGAGATGACGAAAGTCGGATTGTTCTGATTGCCAAGACCACTGTAGCTTCCTGCGAGGAGTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53430.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 21
gtaagcaacccatcaagtatataaataagttgagtgattaccaacagattagagtcttgagt-cctatacctaaatggtgtgttgtgtgatgcagTGTATGCCAAATTGCTATGCAAGGATTATGAGTGTAGGAGATGACGAAAGTCGGATTGTTCTGATTGCCAAGACCACTGTAGCTTCCTGCGAGGAGTTAA
| | |||||| | | | | | | | | | | | ||| | ||||| | | ||||||| | ||||| ||||||||||||||||||||||| || ||||||| || || ||||| || || ||||||| | ||| || || |||| ||| |||
---------gtaaggattatatatacccccctaatcccactctagtttctgaaatagtaaacgcgcatatgatgttttcgtgttttat--tgcagTGCACTCCAAACTGCTATGCAAGGATTATGAGTGTGGGGCATGACGAGAGCCGTATTGTCCTAATCGCCAAGAAAAATGTCTCTGCCGGCGAAGAGCTAA
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G179814_T01 (Zea mays), 3'ss of exon 2
gtaagcaacccatcaagtatataaataagttgagtgattaccaacagat-tagagtcttgagtcctatacctaaatggtgtgttgtgtg-atgcagTGTATGCCAAATTGCTATGCAAGGATTATGAGTGTAGGAGATGACGAAAGTCGGATTGTTCTGATTGCCAAGACCACTGTAGCTTCCTGCGAGGAGTTAA
|| | | || | ||| | | | || | | | | || | | || | || | | |||||||| | ||||| ||||||||||||||||||||||| ||| |||| |||||||| |||||||| || || |||| | || | | || ||| |||
------------------gtaaggaccatatgcctaattccatatatatgtttacctctaaaatagatgctcagttgacctttttttttcatgcagTGCACACCAAACTGCTATGCAAGGATTATGAGTGTTGGACATGATGAAAGTCGTATTGTTCTAATAGCGAAGAAAAAAGTTTGCGCTGGTGATGAGCTAA
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 13
-------------------------gtaagcaaccca--tcaagtatataaataagttgagtgattaccaacagattagagtcttgagtcctat---acctaaatggtgtgttgtgt-gatgcagTGTATGCCAAATTGCTATGCAAGGATTATGAGTGTAGGAGATGACGAAAGTCGGATTGTTCTGATTGCCAAGACCACTGTAGCTTCCTGCGAGGAGTTAA
|| | || | || ||| | | || | || || | | || || || | || | ||| || ||||||||||| |||||||||||||||||||||||||| || ||||| || || |||||||| || || || ||||| ||| || | | || ||| |||
gtaagtgaaccaaaatagttgtatgacaaattgctcaatttttgtgtattattgttacccctgtactctcactaatggttatttgacatctcatcttactattttcttggttcatgtcaatacagTGTATGCCCAATTGCTATGCAAGGATTATGAGTGTGGGTGATGATGAGAGCCGGATTGTACTCATCGCTAAGACTGATGTGTCTACTGGTGATGAGCTAA
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 22
gtaagcaacccatcaagtatataaataagttgagtg-attaccaacagattagagtcttga---------gtcctat-acctaaatggtgtgttgtgt-gatgcagTGTATGCCAAATTGCTATGCAAGGATTATGAGTGTAGGAGATGACGAAAGTCGGATTGTTCTGATTGCCAAGACCACTGTAGCTTCCTGCGAGGAGTTAA
||||| | || | | || | || || || || || | || ||| | ||| | | |||| || | ||| || ||||||||||||||||||||||||||||| |||||||| || ||||| || || |||||||| || || || ||||| | || ||| || | || |||||||
gtaagtcaacctaaacttgaattggcattttctgtacatcactgtcatctcggattctcaacacaggatagtcatcttacctgttctctggttcatgttaatacagTGTATGCCAAATTGCTATGCAAGGATCATGAGTGTCGGTGATGAGGAGAGCCGGATTGTACTCATCGCTAAGACTAACGTGGCTGCCGGTGATGAGTTAA
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 22
-----------------gtaagcaacccatcaagtatataaataagttgagtgattaccaacagattagagtcttgagtcctatacctaaatggtgtgttgtgt-gatgcagTGTATGCCAAATTGCTATGCAAGGATTATGAGTGTAGGAGATGACGAAAGTCGGATTGTTCTGATTGCCAAGACCACTGTAGCTTCCTGCGAGGAGTTAA
|| || | |||||| | | |||| |||| | | | | | ||||| || | ||| || ||||||||||||||||||||||| ||||| |||||||| || || ||||| || |||||||| || ||||| ||||| | || | | || | || |||||||
gtgagtcaacctaaacttgaattgacattttctgtatatctttgtcctctcggattctcaac---tctggataatagttatcttacctgttctttggttcatgttaatacagTGTATGCCAAATTGCTATGCCAGGATCATGAGTGTTGGTGACGACGAGAGCCGGATTGTACTCATTGCTAAGACTAACGTGGTTGCCGGTGATGAGTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accaacagattagagtcttgagtcctatacctaaatggtgtgttgtgtgatgcagTGTATGCCAAATTGCTATGCAAGGATTATGAGTGTAGGAGATGACGAAAGTCGGATTGTTCTGATTGCCAAGACCACTGTAGCTTCCTGCGAGGAGTTAA
acctaaa putative branch site (score: 3)
taaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaacccatcaagtatataaataagttgagtgattaccaacagattagagtcttgagtcctatacctaaatggtgtgttgtgtgatgcagTGTATGCCAAATTGCTATGCAAGGATTATGAGTGTAGGAGATGACGAAAGTCGGATTGTTCTGATTGCCAAGACCACTGTAGCTTCCTGCGAGGAGTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG