Sequence
atgc intronic sequence ATGC exonic sequencegtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34570.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 7
gtcagtagcttctctcttatctcttgacactttctga-gttttggcaaaacag---atttctgtgtcgagacattttg--ttcatctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
|| || ||||| | || | || | || || | | | || | || || | | | | | | | |||| || || || ||||||||||| |||||||| |||| ||||||||||| | ||||| ||| ||||||||||||| |||||||| ||| | || |||||
---gtaagtttttctctcgcccctacatacctatcgatgtaccaatctatctgtccatctaggtctctaaggactaaggactaactatttgtaacagATATACCGACATGCATGCTGACTATACTGGTAAAGGCTTTGATCAGCTAATGGATGTGATTGACAAGATCAAGAATAATCCTGACGATAGGCGAATTATC
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 6
gtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
||| | | | | || | || | | |||| | || ||| | || | | ||| ||| |||| || || || ||||||||||| |||||||| |||| ||||||||||| | ||||| ||| ||||||| ||||||||||||||||| || || || ||
----gtaagcttacattcctttccttgagctgtatctttttt-------cttgttcatgttttctgataaagttgacatatctg---acagATATACTGACATGCATGCTGACTATACTGGAAAAGGCTTTGATCAGCTAATGGATGTGATTGACAAGATTAAGAACAATCCTGATGACCGCCGAATAATT
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 7
gtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
|| || | | |||| |||||| | || | |||| || | | | | || | | | || | |||| ||||| || ||||||||||| ||||| || |||| ||||||||||| | ||||| ||| ||||||||||||| ||||||| || || || || ||
gtaagctacattcctctcctctcttctcgtgttgtctcttttcttttgttc-atgtattttttgataaagtagacatatttg-----acagATACACTGACATGCATGCTGACTATACGGGAAAAGGTTTTGATCAGCTAATGGATGTGATTGACAAGATCAAGAATGATCCTGACGACCGTCGAATAATT
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 6
gtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatct-ctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
|| ||| | | | |||||| ||| | | | | | |||| || || | | || |||||| | | |||||||| || || ||||||||||| || | |||||||||||||||||||| |||||||| ||||||||||| ||| ||||||||||||||||| |||| ||
gtaagtggatgtgcctttatct-ttgtaagtcattaggctgcattttgtaggattgcttagttctg---tatttctcatctacattttacagGTATACTGACATGCATGCTGACTACTCCGGCCAAGGATTTGATCAGCTTTTAGATGTTATTAACAAGATAAAGCACAATCCTGATGATCGAAGGATCATT
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 7
gtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatct-ctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
|| ||| | | | |||||| ||| | | | | | |||| || | | | || |||||| | | |||||||| || || ||||||||||| || |||||||||||||||||||||| |||||||| ||||||||||| ||| | ||||| |||||||| |||| ||
gtaagtggatgtgcctttatct-ttgtaagtcattaggctgcatttcgtaggattgctcagctctg---tatttctcatctacattttacagGTATACTGACATGCATGCTGACTACTCTGGCCAAGGATTTGATCAGCTTTTAGATGTTATTAACAAGATAAAGCATAATCCCAATGATCGAAGGATCATT
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 7
gtcagtagcttctctcttatctcttgacactttctga-gttttggcaaaacagatttctgtgtcgag-------acattttgttca-----tctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
|| | | | | ||| | || || ||| | | | ||| | | || ||||| || || ||| ||| | | | || || || || || |||||| ||| || | || ||||| ||||||||||| |||||||| ||||||||||| ||| | |||||||||||||| || |||||
gtagggaaactatacctttttgttttttttttcctgttggtattacaatagattgttttgtgtggaattgctcaactctttattcgatgccttacattttatagATATACTGACATGCATCATGACTACTCCGGTCAAGGGTTTGATCAGCTTTTAGATGTTATTAACAAGATAAAGCATAATCCTGATGATCGGCGAATTATT
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 7
----gtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
| | || | || ||| || | | || || || || | ||| | | | | |||| || || || || |||||| ||| || | |||||||| |||||||| || |||||||| ||||||||||| ||| |||||||||||||| || || ||
gtaggggaactataccttttttttctgctggtattacaatagattgttttgtgaggaattgctcaactctttattcgctgccttacattctatagATATACTGACATGCATCATGACTACTCCGGCCAAGGGTTTGATCAACTTTTAGATGTTATTAACAAGATAAAGCGTAATCCTGATGATCGGCGAATCATT
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------gtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
|| | ||| | || | ||||| || | | | || || || | ||| |||| | | | ||||| || | || ||||||||||| |||||||||||||||||||||||| | |||||||| ||||||||||||||||| ||||| ||||||||||||||||
gttcgtggattttattctttgaaagtttatgtggtggactctatttttctcgagtaaggattctgttttctcgaggtagtttttctccagttttaacctattgctcatatat-tttacagCTATATTGACATGCATGCTGACTATACTGGCCAAGGATTTGATCAGTTGTTAGATGTTATTAACAAGATCAAGAATAATCCGAATGATCGACGGATTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttggcaaaacagatttctgtgtcgagacattttgttcatctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
ttttgttcatctctct CT-rich tract
attttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatctctctctacagGTACACAGATATGCATGCTGATTATACTGGCCAAGGATTTGATCAGCTCTTAGATGTAATTAACAAGATCAAGAACAATCCTGATGATCGACGGATTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC