Sequence
atgc intronic sequence ATGC exonic sequencegtctgaaatttgtctctttttcccgattactcttgtttcatgattctctctgtctcttcaatctctcaaacaccattcttctcttgttgccttttttcagATTACAGAGCAAATATATGTTGGCTCTTGCATACAAACAGAAGAGGATGTGGAAAACTTGTCGGAAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01510.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g29160.1 (Oryza sativa), 3'ss of exon 3
--------------------------gtctgaaatttgtctctt----tttcccgattactcttgtttcatgattctctctgtctcttcaatctctcaaacaccattcttctcttgttgccttttttcagATTACAGAGCAAATATATGTTGGCTCTTGCATACAAACAGAAGAGGATGTGGAAAACTTGTCGGAAGCT---
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gtaattgtcctcctataactaattagttcttggatgtgcatcaaaagattttaatattaacagtgtttttgtcttgttgatatcctctcaggactttaagcttactcattttccgtatattttttaacagATTACAGAACAAATATTTGTTGGATCATGCCTACAAACAGAAAGAGATGTGAAAATGCTATCAGAGACTATG
upper sequence: AT3G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G08030.1 (Glycine max), 3'ss of exon 3
gt-ctgaaatttgtctctttttcccgattactcttgtttcatgattctctctgtctcttcaatctctcaaacaccattcttctcttgttgccttttttcagATTACAGAGCAAATATATGTTGGCTCTTGCATACAAACAGAAGAGGATGTGGAAAACTTGTCGGAAGCT---
|| || ||| || | | || | | | | || || | | | | ||| |||| | | || ||| | ||| | | | |||||||||||||||||||||| || || || |||||||||||||| ||||| |||| |||||| ||| |
gtattgcaatgtgaatttacttgcttacaattatttgtttaaaagcatactt---tctacaatatttataaa--tattgatatctcataaattcct---agATTACAGAGCAAATATATGTGGGATCCTGTATACAAACAGAAGATGATGTAGAAACCTTGTCAAAAGTTGAG
upper sequence: AT3G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G11100.1 (Glycine max), 3'ss of exon 5
gt-ctgaaatttgtctctttttcccgattactcttgtttcatgattctctctgtctcttcaatctctcaaacaccattcttctcttgttgccttttttcagATTACAGAGCAAATATATGTTGGCTCTTGCATACAAACAGAAGAGGATGTGGAAAACTTGTCGGAAGCT---
|| || ||| || | | || | |||| || ||| | | | | | ||| |||| | | || ||| | || || | || |||||||||||||||||||||| || || || |||||||||||||| ||||| |||| |||||| ||| |
gtattgcaatgtgaatttacttgc---ttacaattatttgtttaatagcatactttctacaatatttataaa--tattgatacctcgtaaattctt---agATTACAGAGCAAATATATGTGGGATCCTGTATACAAACAGAAGATGATGTAGAAACCTTGTCAAAAGTTGAG
upper sequence: AT3G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0066g01200.t01 (Vitis vinifera), 3'ss of exon 3
gtctgaaatttgtctctttttcccgattactcttgtttcatgattctctctgtctcttcaatctctcaaacaccattcttctc-ttgttgccttttttc--agATTACAGAGCAAATATATGTTGGCTCTTGCATACAAACAGAAGAGGATGTGGAAAACTTGTCGGAAGCT
||| | | | || | | | || || || || | | | || | || ||| || | | ||| | ||||| ||||||||||||||||||| || || || ||||| ||||| |||| |||||||||| ||||| | ||
-cctgtccatgggagggagtagatgaagatgccttttcaattgttgtcgaagcatttc--atgttgcatttctaattttttttactattgtttattttcctagATTACAGAGCAAATATACGTAGGATCATGCATCCAAACCGAAGCCGATGTGGAAACTTTGTCAAATGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctctgtctcttcaatctctcaaacaccattcttctcttgttgccttttttcagATTACAGAGCAAATATATGTTGGCTCTTGCATACAAACAGAAGAGGATGTGGAAAACTTGTCGGAAGCT
caccattcttctcttg CT-rich tract
ttttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgaaatttgtctctttttcccgattactcttgtttcatgattctctctgtctcttcaatctctcaaacaccattcttctcttgttgccttttttcagATTACAGAGCAAATATATGTTGGCTCTTGCATACAAACAGAAGAGGATGTGGAAAACTTGTCGGAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG