Sequence
atgc intronic sequence ATGC exonic sequencegtatgcacctctatgtttcacccttctggattctggttatggatttattcaatcattcctttcttatgtatatataatctgaatataaagaacatttgcgattctgttatattttgttacagATCCAAGGTTGACTGACTATGATACACTTCTTGACAATATACATGGTCTAAGGGATGGAAAACCTGTTCAGGTTCCAATATATGACTTCAAGTCGAGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73980.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 2
gtatgcacctctatgtttcacccttctggattctggttatggatttattcaatcattcctttcttatgtatatataatctgaatataaagaacatttgcgattctgttatattttgttacagATCCAAGGTTGACTGACTATGATACACTTCTTGACAATATACATGGTCTAAGGGATGGAAAACCTGTTCAGGTTCCAATATATGACTTCAAGTCGAGTTC
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-------------agtttgattgcttggagctgcattca---attgggagcggcagtggtgctaactaactacttaa-ctgagtt--agtgatgtctg-atctttgtgacatttga--acagATCCACGCCTAACAGACTACGACACACTGTTGGAAAATATTCATGGTCTGAAGGAGGGAAGATCAGTTCAGGTTCCAATATATGATTTCAAGATGAGCTG
upper sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 2
gtatgcacctctatgtttcacccttctggattctggttatggatttattcaatcattcctttcttatgt----atatataatctgaatataaagaacatttgcgattctgttatattttgttacagATCCAAGGTTGACTGACTATGATACACTTCTTGACAATATACATGGTCTAAGGGATGGAAAACCTGTTCAGGTTCCAATATATGACTTCAAGTCGAGTTC
| | || || | ||| | ||| | | ||| | || || | | | | || | |||| | ||| || | ||| |||||||| | |||| |||||||| ||||| || || |||||||||||||| | ||| |||| | |||||||||||||||||||| |||||||| || |
-----------------------gttagtatcagagtgctctattattacaaactgcattctctaaggttataatgtttcctaccagagaaattgatattttcacctct--taaaacttgcc-cagATCCACGTCTGACAGACTATGACACACTGCTGGAAAATATACATGGTCTGAAGGAAGGAAGGTCAGTTCAGGTTCCAATATATGATTTCAAGTCAAGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatatataatctgaatataaagaacatttgcgattctgttatattttgttacagATCCAAGGTTGACTGACTATGATACACTTCTTGACAATATACATGGTCTAAGGGATGGAAAACCTGTTCAGGTTCCAATATATGACTTCAAGTCGAGTTC
ttttgtt CT-rich tract
tataatctgaatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcacctctatgtttcacccttctggattctggttatggatttattcaatcattcctttcttatgtatatataatctgaatataaagaacatttgcgattctgttatattttgttacagATCCAAGGTTGACTGACTATGATACACTTCTTGACAATATACATGGTCTAAGGGATGGAAAACCTGTTCAGGTTCCAATATATGACTTCAAGTCGAGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA