Sequence
atgc intronic sequence ATGC exonic sequencegtttgttttactttctcttcttgaattagttttgtacattcttcttcttgcttttgaatatgatgaattttgatagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48330.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g44280.2 (Oryza sativa), 3'ss of exon 2
-----------------------gtttgttttactttctcttcttgaattagttttgtacattcttcttcttgcttttgaatat--gatgaattttgatagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA
| | | || | | |||| | | | ||| || | || | ||| || || | ||| || |||||| |||| |||||||| ||| ||||||||||| | |||||||| || ||||||| |||||||| || || ||||| |||| ||| || |
gtttaatatttcctagctgaaatgctcaacagatagcaaatttctatacatgtttgtcaactcgcattgcttatttacgtatctttgat-aacttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTTGAACATATCCCAGAGTTGGTTACTTCGTCTATTGA
upper sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 3
------------------gtttgttttactttctcttcttgaattag---ttttgtacattcttcttcttgct--tttgaatatgatgaattttg-atagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA
|| | | | | ||||| ||| | | || | |||| |||| | |||| ||||| ||| || || ||| |||||||||||||||| | ||||||||| | |||||||| || ||||||| |||||||| || || ||||| ||| ||||| | |
tgccaggcagttatcccagtccacgaagcaagcaggccctatattagatatttgttgtttaactcattttgcctgtttgtttctgatttattttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA
upper sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G13480.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------------------------------------------------gtttgttttactttctcttcttgaattagttttgtacattcttcttcttgcttttgaatatgatgaattttgatagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA
| | | | || || | || | | |||| || || | || | ||| || || ||| | ||||| |||||||| | ||||||||| ||||||| |||||||||||||||||||||||||||||||||| ||| ||| || |
gtgtgaagattttataatgtaaaaccttgactgtgacaattagttttctctcatagatttgcataatcccaattcaatgcggaaacgttgtacgtaccacacacagatttaacaggaatggaactttaatgcatttttctctgcattctcttcatttgatgcgcaatattcatattttggacccctttacagGAACGGGATACCTGACTGCATGCTTTGCCTTGATGGTTGGACCCGAAGGCCGTGCTATTGGTGTGGAACATATTCCTGAATTGGGTTCTTTTTCAATTGA
upper sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G02810.1 (Glycine max), 3'ss of exon 2
------------------------gtttgttttactttctcttcttgaattagttttgtacattcttcttcttgcttttgaatatgatgaattttgatagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA
|| ||| | | || || | | || | | |||| || | | || ||| || || ||| | || || |||||||| | ||||||||| || |||| ||||||||||| ||||||||||||||||| ||||| ||| ||| | |
tgctactatatagatttaactggagtggaatttcaatgcattttttctctgaattctctgcatttgatgcacaatgttcatactttggacccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCCGTGCTATTGGCGTGGAACATATTCCTGAGTTGGTTTCTTTTTCAATCGA
upper sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G36430.1 (Glycine max), 3'ss of exon 2
-------------gtttgttttac--------tttctcttcttgaat---tagttttgtacattcttcttcttgcttttgaatatgatgaattttgatagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA
| ||||| || ||| ||| | || || ||| | | || ||| ||| | | | | || ||| || |||||| | ||||| |||||||| | |||||||| || |||| |||||| |||||||||| ||||||||||| |||||| ||| ||| | |
ggaccaacttgtgttctgtttcaccataggtttttggcttttcacatttttatctttatttggtgttgttcacaatttccacatttgggcctatttgcagGAACGGGGTACCTGACTGCATGCTTTGCCTTGATGGTTGGGCCCCAAGGCCGTGCTGTTGGTGTGGAGCATATTCCTGAGTTGGTGTCTTTTTCAATAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaattagttttgtacattcttcttcttgcttttgaatatgatgaattttgatagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA
aatatgatgaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttttactttctcttcttgaattagttttgtacattcttcttcttgcttttgaatatgatgaattttgatagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG