Sequence
atgc intronic sequence ATGC exonic sequencegtacctattgttgtatctttgcgtttaaaatatctcgtatccttgccctgcttatctgaggttcttctattctcactttctcagGGTGCTAATATCCTTGTGGATAATCAAGGATGCATTAAACTTGCTGATTTTGGTGCGTCCAAACAGGTAGCGGAGTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54960.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g21510.1 (Oryza sativa), 3'ss of exon 5
gtacctattgttgtatctttgcgtttaaaatatctcgtatc----------cttgccctgcttatctgaggttcttctattctcactt---tctcagGGTGCTAATATCCTTGTGGATAATCAAGGATGCATTAAACTTGCTGATTTTGGTGCGTCCAAACAGGTAGCGGAGTTG
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gtactcaaaatctgaattctgaacacacaataatatgtatttattttaccacttgttgtgctcattatgattattcctgttatttgtcaaattccagGGAGCGAACATTCTTGTTGATAACAAAGGATGCATTAAACTTGCTGATTTTGGGGCATCTAAGCAAGTGGCAAAGTTG
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G098828_T01 (Zea mays), 3'ss of exon 5
-------------gtacctattgttgtatctttgcgtttaaaatatctcgtatccttgccctgcttat-ctgaggttcttcta---ttctcactttctcagGGTGCTAATATCCTTGTGGATAATCAAGGATGCATTAAACTTGCTGATTTTGGTGCGTCCAAACAGGTAGCGGAGTTG
| || | | || ||| | | || |||| ||||||| || | | ||| | || | | ||||||||| || || ||||| |||||| |||| ||||| ||||||||||||||||| || || || || || || |||||
gtatgcacgttgaagtcttaatatataatgcagatatttggccttgtttgttctgttgcaatgcttattctaatgaacttgaaaattttgccaaatttcagGGTGCAAACATTCTTGTTGATAATAAAGGGTGCATCAAACTTGCTGATTTTGGGGCATCTAAGCAAGTTGCAAAGTTG
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC197029.3_FGT003 (Zea mays), 3'ss of exon 5
gtacctattgttgtatctttgcgttta-----aaatatctcg-tatccttgccctgctta-----tctgaggttcttct--attctcactttctcagGGTGCTAATATCCTTGTGGATAATCAAGGATGCATTAAACTTGCTGATTTTGGTGCGTCCAAACAGGTAGCGGAGTTG
||| | | ||| | | || | || | | | | | |||| ||| | | ||| | | | | ||| || | ||||||||| || || ||||| |||||| |||| ||||| ||||||||||||||||| || || || || || || |||||
gtatgaacactgaagccttaacatataatggcagatctttggctttgcttgttctgttgaatgcttctaatgaaccttgaaattttccaaatttcagGGTGCAAACATTCTTGTAGATAATAAAGGGTGCATCAAACTTGCTGATTTTGGGGCATCTAAGCAAGTGGCAAAGTTG
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 5
-----------gtacctattgttgtatc-tttgcgtttaaaatatctcgtatccttgccctgcttatctgaggtt--cttctattctcacttt---ctcagGGTGCTAATATCCTTGTGGATAATCAAGGATGCATTAAACTTGCTGATTTTGGTGCGTCCAAACAGGTAGCGGAGTTG
| || | | || | | ||| | |||| ||| | | | ||| | | | | | | |||| | | |||| || || ||||| || |||||| ||||||||||||||||||| ||||||||||| ||||| ||||| | |||| ||
gtgctgtctctctttctccccctctctcactctcacttattctctctcttatttcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatctcgtatccttgccctgcttatctgaggttcttctattctcactttctcagGGTGCTAATATCCTTGTGGATAATCAAGGATGCATTAAACTTGCTGATTTTGGTGCGTCCAAACAGGTAGCGGAGTTG
ttctcac putative branch site (score: 2)
ttcttctattctcact CT-rich tract
ttctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctattgttgtatctttgcgtttaaaatatctcgtatccttgccctgcttatctgaggttcttctattctcactttctcagGGTGCTAATATCCTTGTGGATAATCAAGGATGCATTAAACTTGCTGATTTTGGTGCGTCCAAACAGGTAGCGGAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT