Sequence
atgc intronic sequence ATGC exonic sequencegtgagtaacttccagaaattgtgttgctgatgatagaaaaactctagttatggttttaagttaacgaaataattttatctgttcagtttttactctcaaatttatttaccgttcttttcggttgttttcagTGAGCTGGTGGGTCTATTTTTTCCTGCTGTAACAGGAATTATGGCTGGTTCAAATCGATCAGCTTCACTTAAAGATACACAAAAATCAATTCCTGTTGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30450.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 8
----gtg-agtaacttccagaaattgtgttgctgatgatagaaaaactc-tagttatggttttaagttaacgaaataattttatctgttcagtttttactctcaa-atttatttaccgttcttttcggttgt----tttcagTGAGCTGGTGGGTCTATTTTTTCCTGCTGTAACAGGAATTATGGCTGGTTCAAATCGATCAGCTTCACTTAAAGATACACAAAAATCAATTCCTGTTGGT
| | | | | ||| | || || | | ||| | ||| | | | | || | ||| || | | | ||| || ||| || | || | || | ||| | |||||||| || | ||||| | || || || || |||||||| ||||||||||||||||| || |||||||| ||||| |||||| ||||| || ||||
gtctatatattgggattttaagtctgtcctccttttgttgttgatacttgtttttaagatcctctaattacttgcaattttcatttatcgattttgtagattcagtatgcacttgctaacattctttgttttgttctttcagTGCTTTGTTAGGTCTCTACTTCCCAGCAGTTACAGGAATCATGGCTGGTTCAAATCGGTCTGCTTCACTGAAAGACACACAACGTTCAATACCAATTGGA
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G088761_T01 (Zea mays), 3'ss of exon 2
gtgagtaacttccagaaattgtgttgctgatgatagaaaaactctagttatggttttaagttaacgaaataattttatctgttcagtttttactctcaaatttatt-taccgttcttttcg-gttgtt--ttcagTGAGCTGGTGGGTCTATTTTTTCCTGCTGTAACAGGAATTATGGCTGGTTCAAATCGATCAGCTTCACTTAAAGATACACAAAAATCAATTCCTGTTGGT
| || | || || | || |||||| | ||| ||| | ||| | | || || |||||| | | |||| | | | | ||||||| |||| ||||| ||||| || || || || |||||||||||||| ||||| ||||| |||||||| ||||||||||| || || || | ||
-------------------------------aagagcatgaccctgttcat--ttttaaatgcacgg--ccgtttgcacatttccttatgtatgtgaaactttattgtgctaaattttttgtatcgatccttcagTGCTTTGGTAGGTCTGTTTTTCCCAGCAGTCACTGGAATTATGGCTGGCTCAAACCGATCTGCTTCACTGAAAGATACACAGCGTTCGATACCAATCGGC
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G113276_T02 (Zea mays), 3'ss of exon 3
gtgagtaacttccagaaattgtgttgctgatgatagaaaaactctagttatggttttaagttaacgaaataattttatctgttcagtttttactctcaaatttatt----taccgttcttttcggttg---ttttcagTGAGCTGGTGGGTCTATTTTTTCCTGCTGTAACAGGAATTATGGCTGGTTCAAATCGATCAGCTTCACTTAAAGATACACAAAAATCAATTCCTGTTGGT
| | | | | |||||| | ||| | ||| | | | | | || || |||||| || | || |||| | | |||||||| ||||| ||||| ||||| || || || || |||||||||||||| ||||| ||||| || ||||| ||||||||||| ||||| || | ||
------------------------------------ttacctttttgctgcatttttaaatgcacgg--cagtttgcacattgccttatgtatgtgaaactttattgtgctaacattttttttgtatcaatctttcagTGCTCTGGTAGGTCTCTTTTTCCCAGCGGTCACTGGAATTATGGCTGGCTCAAACCGATCTGCCTCACTGAAAGATACACAGCGTTCAATACCAATCGGC
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 8
gtgagtaacttccagaaattgtgttgctgatgatagaaaaactctagttatggttttaagttaacgaaataattttatctgttcagtttttactctcaaatttatttaccgttcttttcggttgttttcagTGAGCTGGTGGGTCTATTTTTTCCTGCTGTAACAGGAATTATGGCTGGTTCAAATCGATCAGCTTCACTTAAAGATACACAAAAATCAATTCCTGTTGGT
| ||||| || | | || | | || |||| | || | | || || | | || | || ||| ||| || | |||| |||| || || ||||| |||||||| || ||||| ||||| ||||| ||||||||| | || || | |||||| || ||||||||||||||||
------------------------cattcatgattaaagcatgttccctagagccc-attttgttgaaaaatttgctagtttatgattcatattttttaactg---taatattccttt---ttcctcccagTTCATTGGTTGGCCTCTTTTTCCCTGCTGTGACGGGAATAATGGCAGGTTCTAATCGATCATCCTCTCTGAGAGATACTCAGCAATCAATTCCTGTTGGA
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 9
gtgagtaacttccagaaattgtgttgctgatgatagaaaaactctagttatggttttaagttaacgaaataattttatctgttcagtttttactctcaaatttatttaccgttcttttcggttgttttcagTGAGCTGGTGGGTCTATTTTTTCCTGCTGTAACAGGAATTATGGCTGGTTCAAATCGATCAGCTTCACTTAAAGATACACAAAAATCAATTCCTGTTGGT
|| | || ||| | | || || |||| ||| | | || ||||||| | | |||| | || || | | |||||| | || |||||| ||||| ||||||||||| ||||||||||| ||||||||||| ||||||||||| || |||||| | | ||| || ||| ||||||||||||||
---------------gaactatgatgcatgccaacctattacattacaaatgggtttgaaatg--gagttaattttcttaat--ggttt-----------tctaactatcctacttttca-ctattgtcagTGCACTGGTCGGTCTATTTTTCCCTGCTGTAACGGGAATTATGGCAGGTTCAAATCGCTCTGCTTCATTGAGAGACACTCAACGTTCAATTCCTGTTGGA
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S5_444V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgagtaacttccagaa-attgtgttgctgatgatagaaaaactctagttatggttttaagttaacgaaataattttatctgttcagtttttactctcaaatttatttaccgttcttttcggttgttttcagTGAGCTGGTGGGTCTATTTTTTCCTGCTGTAACAGGAATTATGGCTGGTTCAAATCGATCAGCTTCACTTAAAGATACACAAAAATCAATTCCTGTTGGT
|| || || | | ||| | | | | || | | || | || | || || | || ||| | | || |||| | ||| || | | | || || ||| | || | || ||||||||||||||||| || || |||||||| || ||||| || |||||||| || || ||||| || || ||||| ||
gtatgtcaccacttttacatttaggtcaagttaatcaacactttcaaattgcacctacaaaatag-aatatgattctctagcttagattttgtgagggatgcttacttctgatgtgacttgtatgattacagAAACCTACTTGGCCTATTTTTTCCTGCTGTCACTGGGATTATGGCAGGGTCAAACCGTTCAGCTTCTCTGAAGGATACTCAGCGTTCCATTCCCAAGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgttcagtttttactctcaaatttatttaccgttcttttcggttgttttcagTGAGCTGGTGGGTCTATTTTTTCCTGCTGTAACAGGAATTATGGCTGGTTCAAATCGATCAGCTTCACTTAAAGATACACAAAAATCAATTCCTGTTGGT
ttgttttc CT-rich tract
tttttactctcaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtaacttccagaaattgtgttgctgatgatagaaaaactctagttatggttttaagttaacgaaataattttatctgttcagtttttactctcaaatttatttaccgttcttttcggttgttttcagTGAGCTGGTGGGTCTATTTTTTCCTGCTGTAACAGGAATTATGGCTGGTTCAAATCGATCAGCTTCACTTAAAGATACACAAAAATCAATTCCTGTTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT