Sequence
atgc intronic sequence ATGC exonic sequencegtacatgttaatcttttcagcctgtttctgtgaacatgtctgtgcaggcattatgttcttttatatttcagcaaggactttgcaatttttattccctacaacaatttaacatcaagttaatttggctcagGTACTATTCTAGCTTGGAAGTTGCTGCTGAGTATTTCAGATCCGGTGCTGATAAGATCTCCATAGGAAGTGACGCTGTTTCTGCTGCAGAGGAGTTCATA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26900.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 13
--gtacatgttaatcttttcagcctgtttctgtgaac-atgtctgtgcaggcattatgttctttt---atatttcagc--aaggactttgcaatttttattccctacaacaatttaacatcaagttaatttgg-----------ctcagGTACTATTCTAGCTTGGAAGTTGCTGCTGAGTATTTCAGATCCGGTGCTGATAAGATCTCCATAGGAAGTGACGCTGTTTCTGCTGCAGAGGAGTTCATA
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gtattattactgatcattatgga--gattatgctattgactttcttgcattctttcccctctattgaaattattcagtcttatagttttatcaattgtgttccct-cagaattttcaaatctttttgatccgatcaattatattctcagGTACTATTCTAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
upper sequence: AT4G26900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 13
--gtacatgttaatcttttcagcc-tgtttctgtgaacatgtctgtgcaggcattatgttctttt---atatttcagc--aaggactttgcaatttttattccctacaacaatttaacatcaagttaatttgg-----------ctcagGTACTATTCTAGCTTGGAAGTTGCTGCTGAGTATTTCAGATCCGGTGCTGATAAGATCTCCATAGGAAGTGACGCTGTTTCTGCTGCAGAGGAGTTCATA
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gtattattattgatcattatggagattatgctattgacat-tct-tgcatttttttccctctattgaaattattcagtcttatagttctatcaattgtgttccct-cagaattttcaaatctttttgatccgatcaattatattctcagGTACTATTCAAGTTTGGAAGTTGCTTCTGAATACTTTAGGTCTGGGGCTGATAAGATTTCCATTGGAAGTGATGCAGTTTATGCTGCAGAAGAATATTTA
upper sequence: AT4G26900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------gtacatgttaatcttttc-agcctgtttctgtgaacatgtctgtgcaggcattatgttcttttatatttcagcaaggactttgcaatttttattccctacaaca-----atttaacatcaagttaatttgg--ctcagGTACTATTCTAGCTTGGAAGTTGCTGCTGAGTATTTCAGATCCGGTGCTGATAAGATCTCCATAGGAAGTGACGCTGTTTCTGCTGCAGAGGAGTTCATA
| ||| |||||| | | ||| | | | | | | ||||| || | ||||| | ||| || | ||| | ||| | | || ||| | |||||||| |||||||| |||||||||||| | || |||||||| || || || ||||| || || || |||||||| || |||| |||||| || || | |||
gtacacacttgggtgttgttttctggatgattgtcgttcttttttaatttatttttatcttt-tatttttttttattaaatgttaattc-tccttcagtgattttcttgagatgaaagtgaactattatggatacattatattttaaaccaatctcttcctcagGTATTATTCTAGTTTGGAAGTTGCTTCAGAATATTTCAGGTCAGGGGCAGATAAAATTTCTATTGGAAGTGATGCAGTTTATGCTGCTGAAGAATATATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactttgcaatttttattccctacaacaatttaacatcaagttaatttggctcagGTACTATTCTAGCTTGGAAGTTGCTGCTGAGTATTTCAGATCCGGTGCTGATAAGATCTCCATAGGAAGTGACGCTGTTTCTGCTGCAGAGGAGTTCATA
aatttaacatcaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatgttaatcttttcagcctgtttctgtgaacatgtctgtgcaggcattatgttcttttatatttcagcaaggactttgcaatttttattccctacaacaatttaacatcaagttaatttggctcagGTACTATTCTAGCTTGGAAGTTGCTGCTGAGTATTTCAGATCCGGTGCTGATAAGATCTCCATAGGAAGTGACGCTGTTTCTGCTGCAGAGGAGTTCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG