Sequence
atgc intronic sequence ATGC exonic sequence...tatctatctagcctagaggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73990.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g49570.1 (Oryza sativa), 3'ss of exon 8
tatctatctagcctagaggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
| || ||| || |||| | ||| | | | | || |||| | || || || || | | | || |||||| |||| || ||| || ||||| || || || || |||| |||||||| ||||| || |||||||| || |||||||||||||||||||||
--------------gtaagttatgc-----ttcagatttcaccaatttattag--cagcagagtttcgttatg-tattggttgttgttatttgaac-tagGATGTGGCGGGAAATTCGACTCCTAGCTGACACCAAGCCTGTGGTTGCTTCAATGTCTGATGTTGCTGCAAGTGGTGGGTACTACATGGCAATGGCTGCA
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G122843_T02 (Zea mays), 3'ss of exon 13
tatctatctagcctagaggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatct-tcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
| | |||| | | ||| ||||| | | ||| | | | || ||| ||| | | | | | | || | || |||||||| || ||| ||| || || | | ||||| || |||| || ||||| ||||| || |||||||| ||||||||||||||||||||||||
-gtaagttacgccttaggatttagtg---atttgcttct--cagcagcagcag-cagcagagttttttcagtaacatattacgaattcttatttcaactagGATGTGGAGAGAAATCCGACTTCTAGCCAACTCTAAACCTGTAGTTGCTTCGATGTCTGATGTTGCTGCAAGTGGGGGCTACTACATGGCAATGGCTGCA
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G09020.2 (Glycine max), 3'ss of exon 1
--tatctatctagcctagaggtcatg----tgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
| ||||| || |||||| | || | | | || ||||| | | || | || | ||||| || || || | ||| | | ||| |||||||| || |||| || ||||||| ||||||| |||||||| |||||||| |||||||||||||||||||| |||||||||||||||| |||
aaaacttatctgatcttt--gtcatgaaattatgatgctaagtgcaagtattttggtgagtttgcttg-tttaactataaagtt--ttgtt-gtcatgatctgcagGATGTGGAGAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCA
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G07540.1 (Glycine max), 3'ss of exon 9
tatctatctagcctagaggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA---------
| | | | || | ||| || | | | || |||| | || | || | ||||| || | || | ||| | | | | |||||||| || |||| || ||||||| ||||||| |||||||| |||||||| |||||||||||||||||||| |||||||||||||||| |||
-gtgatctttgtcatgaaattatg-atg---ctaagtgcaagtattttgttgagttcgcttg-tttaagtataaagtt---tttttgtcatgatcttctggatgtggagAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCAGGAGTTATT
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 9
-----tatctatctagcctagaggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
|| ||||| | | |||||| | || | | || |||| || | | | | | | || || || | | ||| || | ||| |||||||| || ||| || |||||| ||||||| |||||||| |||||||| |||||||||||||||||||| |||||||||||||||| ||
tttcaaatacatctacaattgttgtcatgatgacagttttgctaagta-ttttgttgatgatgccaagaatcttgatcattatc-tggtgcatgatc---tgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCGGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 8
tatctatctagcctag--aggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
|| ||| | | | || | ||| |||||| || | ||| | | || | | || ||||| | || | ||| | | ||| |||||||| || ||| || |||||| ||||||| |||||||| |||||||| |||||||||||||||||||| |||||||||||||||| ||
-atgatgatagttttgctaagttttctgttgatttgcatgtt-taggtgatcatattatgatgccaagaatcctaatcattatatggtgtcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv17s0000g04690.t01 (Vitis vinifera), 3'ss of exon 4
tatctatctagcctagaggtcatgtgtggatttgaatttaata--gctttggaaatccttctaggctttatta--taatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
| | || | | | | | || ||| || | || | |||| || | || | || | | | || || || ||| ||||||||||||||| |||| ||| ||||||| ||||||| |||||||| |||||||| |||||||| || || ||||| |||||||||||||||| |||
-gcttgtacagatgaaaaaaga-gaaggaatgagaaaagaaaaatgcatgacaaatataatgagctcccactaattggtccttaatttttatgat--tatgcagAATGTGGAGGGAAATCAGACTTCTGGCTGCCTCAAAACCTGTCATTGCATCAATGTCTGATGTGGCTGCTAGCGGAGGGTACTACATGGCAATGGGAGCA
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S25_21V6.1 (Physcomitrella patens), 3'ss of exon 11
tatctatctagcctagaggtca-tgtgtggatttgaatttaatagctttggaaatccttctaggctttatta-taatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
|| | || | | ||| | | | | | | | | | | | || ||| | | || | || | | | || || |||||| |||| |||||||| || ||||||| ||| || || ||||| |||||| | || || ||||| |||||||||||||||||||||||||| ||
--cgtaaaaaagctgcttataactgtattgttgtcagtgcatcaattacgttaccgttttcctacttctgaacttataatttttcgttgttacggccattagGATGTGGCGGGAAATCAAACTCCTAGCTGAAAGAAAGCCAGTGATTGCATCAATGGCCGACGTAGCAGCTAGTGGAGGCTACTACATGGCAATGGCAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
tttattataatcttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatctatctagcctagaggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - gatttga
- - - - - - - - - - - - - - - - - - - - - -gctttgg