Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatttggtatgcaaaataatttataatcttttggtcctgaaacgtattataagtttttcaatactgaatatttctgatgcagATGGATTCTTCTGGAAGTTGTTGATAAGGTCTATCCAGGCTCAGTTAACTGGAAGCAGGCTTCAAAACCACCAATTAAGATGCCGTTTAGAAAAGTAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55400.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55400.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G556845_T01 (Zea mays), 3'ss of exon 9
gtaagcatttggtatgcaaaataatttataatcttttggtcctgaaacgtattataagtttttcaatactgaatatttctgatgcagATGGATTCTTCTGGAAGTTGTTGATAAGGTCTATCCAGGCTCAGTTAACTGGAAGCAGGCTTCAAAACCACCAATTAAGATGCCGTTTAGAAAAGTAGAG
| | || | || | | | ||||||| | | | || | | | | ||||| |||||||| || | || || ||| |||| || | | |||||| ||||||||||||||||| || || ||||||||||| | |||||||||||||| || ||
----gtaagacacatttgtagcaaaaaaaatttttttggt----atatatgttgctacctcaccggagtgg--tattt-----gcagATGGGTTTTGCTAGAGGTTCTTGACAAAATTTCTCCAGGGTCAGTTAACTGGAAGCATGCATCCAAACCACCAATCATTATGCCGTTTAGAAAGGTTGAA
upper sequence: AT5G55400.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
--gtaagcatt----tggtatgca-aaataattt-ata-atcttttggtcctgaaacgtatta--taagtttttcaatactgaatatttc-tg-atgcagATGGATTCTTCTGGAAGTTGTTGATAAGGTCTATCCAGGCTCAGTTAACTGGAAGCAGGCTTCAAAACCACCAATTAAGATGCCGTTTAGAAAAGTAGAG
||| || ||| | ||| ||| ||||| || | ||| | || || | || || ||| | || | | | | || || |||||||||||| || ||||||| |||| ||||| | |||||| || ||||||||||||| || |||||||| || ||||||||||| || ||||||||||||
aaataatttttgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttggtcctgaaacgtattataagtttttcaatactgaatatttctgatgcagATGGATTCTTCTGGAAGTTGTTGATAAGGTCTATCCAGGCTCAGTTAACTGGAAGCAGGCTTCAAAACCACCAATTAAGATGCCGTTTAGAAAAGTAGAG
ttctgat putative branch site (score: 3)
tatttct CT-rich tract
tattataagtttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatttggtatgcaaaataatttataatcttttggtcctgaaacgtattataagtttttcaatactgaatatttctgatgcagATGGATTCTTCTGGAAGTTGTTGATAAGGTCTATCCAGGCTCAGTTAACTGGAAGCAGGCTTCAAAACCACCAATTAAGATGCCGTTTAGAAAAGTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG