Sequence
atgc intronic sequence ATGC exonic sequencegtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatcgttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65930.2 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
------------gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatcgttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
|| | | | | |||| | | | || || |||| ||| | | | | | || | |||||| | || || ||||| || ||||| ||||| ||||| || ||||| ||||| ||||||||||||||||||||||| || || ||||| ||| | ||
gtgaccttttttttaacacttctttttaac-atacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
----------------gtattattgatat--gtaactgtgttcatttacctttcatcctttg--ttattttcttgtggttactaacatcgttttcctttta------acagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
||| || | | | | | || || ||| || | | | || || |||| | | || || |||| ||||| ||||||| || ||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| || | ||
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
-------------------------------------------------gtattattgatatg-taactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatc-gttttcctttta----acagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
| ||||| || | | || ||||| | | ||| | | | ||| | || || ||| ||| || | |||||| ||||||| || ||||| ||||| ||||| || || || ||||| ||||| ||||||||||||||||| ||||||||||| ||||| || | ||
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 19
--------gtat-tattgatatgtaactgtgttcatttacctttcatcctttgttat-----tttcttgtggttactaacatcgttttcc----ttttaa--cagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
| || | | | || | | ||||| | | | | | | | ||| | | || || | | || || ||||||||||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||||||||| |||||||| || || || || ||||| ||| | ||
gtatttgaggatacaaaggcaagtcatttatcatatttatttcttgtttatgggaacatatataacttacactcattatcaatttctcgtggatttgcaatgcagTATTTGGTGCAGTCTGCTGTAGATGGTTATAATGTTTGCATATTTGCCTATGGTCAAACTGGCTCTGGAAAGACATTTACAATCTATGGATCTGACAACA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
gtattattgatatgtaactgtgttcatttacctttcat-----cctttgttattttcttgtggttactaacatcgttttccttttaa---cagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
| | ||| || ||| || |||| | || | | | | | || | | |||| || || | ||| | ||||||||||| || || ||||||||||| ||||| |||||||| ||||| |||||||||||||| |||||||| || || || || ||||| || | ||
--gcaagtcata---aattgtatttatttcttgcttatggaaacatatataacttacac-tcattaccaatttctcgtgtatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 19
--------------------gtattattgatatgtaactgtgtt--catttacctttcatcctttgttat-tttcttgtggttactaacatcgttttccttttaa------------cagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA-------
|| || | | | | | | | ||| ||| || | | | || ||| || | | | || || ||||| ||||| ||||| || || || || ||||| ||||| ||||| |||||||| ||||| ||||||||||||||||||||||| ||||| || || ||||| ||| | ||
gtcttagtataacaaattatagatcatagttttttgctttagatagcatatacattgaaatggatttaatattttttatactcattaccaatgtttttcttttggaaatttgcaatgcagtacttagTGCAATCTGCTGTGGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGTTCTGGAAAGACTTTTACAATCTATGGAGTTGAAAACAATCCTGG
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 19
--------------------------gtattattgatatgtaactgtgttcatttacctttcatc--ctttgttattttcttgtggttactaacatcgttttccttttaa------------cagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
| || | | || | || ||| || | ||| |||||| | | | | || | ||||| ||||| ||||| || || || || ||||||||||| ||||| |||||||| ||||| || ||||||||||||||||| || ||||| || || ||||| ||| | ||
gcaagtcttagtataacaaattaaagatcctagttttttgctttagataatatgtacattgaaatagatttaatatttttctatactcattactaatgtttttcttttggacatttgcaatgcagTACTTAGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTACGGTCAAACTGGTTCTGGGAAGACTTTTACAATCTATGGAGCTGAAAACA
upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
--------gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatc-gttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
|| || || | | | || || ||| || || || || | || || | || | | ||||||||||| || |||||||||||||| ||||| || ||||| |||||||||||||| |||||||||||||| || ||||| || ||||| ||| | |
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttcatcctttgttattttcttgtggttactaacatcgttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
tactaac putative branch site (score: 0)
catcgttttcctttt CT-rich tract
tttgttattttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatcgttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA