Sequence
atgc intronic sequence ATGC exonic sequence...tttctttggaagctatatacccataaacttaaaatgaataaagatggaagctttagctgatataatttgggtgtttctttctttcttccttggtgtgaagCTGTTTCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G15165.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G15165.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G31360.3 (Glycine max), 3'ss of exon 1
--tttctttggaagctatatacccataaacttaaaatgaataaagatggaagctttagctgatataatttgggtgtttctttctttcttccttggt---gtgaagCTGTTTCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT
|| ||| | || | ||| || | | || | | || || | |||| || || | | | || | ||||||||||||| || ||||| || || || || |||||||| |||||||| ||||| ||||| || |||||||| ||||| |||||||
aaaagtattagaattttaattctttcctcctttttgcatcaaactaggaaatacctgtttaattcctttcatttccatcttgctactttgcatagatcagTAATCAGAGATCAAAATGTCTCGAAGATATGACAGCCGTACAACAATCTTCTCCCCGGAAGGACGTCTTTACCAAGTGGAATATGCAATGGAGGCTATTG-----
upper sequence: AT4G15165.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G43710.2 (Glycine max), 3'ss of exon 1
tttctttggaagctatatacccataaacttaaaatgaataaagatggaagctttagctgatataatttgggtgtttctttctttcttccttgg--tgtgaagCTGTTTCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT---------------------
| | ||| | || | ||| || || | || | | |||| |||| | | | |||| | || |||| |||||||| || |||||||| || || || |||||||| || ||||| ||||| ||||| || |||||||||||||| || ||||| |||
----------------tttctcatttattttctttttcctaag-------ctatactttattcattcctctcctttccttctgtttgcgttggactaaaaactcagatcaatatgtctcgaagATATGATAGCCGTACTACAATCTTCTCCCCTGAAGGACGTCTTTACCAAGTGGAATATGCTATGGAGGCCATTGGGAATGCTGGTACTGCAATAGGGATC
upper sequence: AT4G15165.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G43710.1 (Glycine max), 3'ss of exon 1
tttctttggaagc-tatatacccataaacttaaaatgaataaagatggaagctttagctgatataatttgggtgtttctttctttcttccttgg--tgtgaagCTGTTTCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT----
|||| | | || | | | ||| | || | ||| || || | || | | |||| |||| | | | |||| | || |||| |||||||| || |||||||| || || || |||||||| || ||||| ||||| ||||| || |||||||||||||| || ||||| |||
cttctataggagtgccttttctcatttattttctttttcctaag-------ctatactttattcattcctctcctttccttctgtttgcgttggactaaaaactcagATCAATATGTCTCGAAGATATGATAGCCGTACTACAATCTTCTCCCCTGAAGGACGTCTTTACCAAGTGGAATATGCTATGGAGGCCATTGGGAATGCTG
upper sequence: AT4G15165.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G06350.2 (Glycine max), 3'ss of exon 1
tttctttggaagctatatacccataaacttaaaatgaataaagatggaagctttagctgatataatttgggtgtttctttctttcttccttggtgtgaagCTGTT-----TCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT
|| ||| | || | | | | |||| |||| | | | | ||| | | ||| | | | | || || ||||||||||||| || ||||| || || || || |||||||| || ||||| ||||| ||||| || |||||||| ||||| |||||||
aagtattagaattttaattctttctctcctttttgcatcaaagtaggaaatacctgtttaatttctttcattttcatttttgctacttttcatagatcagTAGTCAGAGATCAAAATGTCTCGAAGATATGACAGCCGTACAACAATCTTCTCCCCTGAAGGACGTCTTTACCAAGTGGAATATGCAATGGAGGCTATTG-----
upper sequence: AT4G15165.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G31360.2 (Glycine max), 3'ss of exon 1
-------tttctttggaagctatatacccataaacttaaaatgaataaagatggaagctttagctgatataatttgggtgtttctttctttcttccttgg---tgtgaagCTGTTTCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT
|| ||| | || | ||| || | | || | | || || | |||| || || | | | || | ||||||||||||| || ||||| || || || || |||||||| |||||||| ||||| ||||| || |||||||| ||||| ||
gaaaaaaaagtattagaattttaattctttcctcctttttgcatcaaactaggaaatacctgtttaattcctttcatttccatcttgctactttgcatagATCAGTAATCAGAGATCAAAATGTCTCGAAGATATGACAGCCGTACAACAATCTTCTCCCCGGAAGGACGTCTTTACCAAGTGGAATATGCAATGGAGGC----------
upper sequence: AT4G15165.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G06350.1 (Glycine max), 3'ss of exon 1
-----tttctttggaagctatatacccataaacttaaaatgaataaagatggaagctttagctgatataatttgggtgtttctttctttcttccttggtgtgaagCTGTT-----TCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT
|| ||| | || | | | | |||| |||| | | | | ||| | | ||| | | | | || || ||||||||||||| || ||||| || || || || |||||||| || ||||| ||||| ||||| || |||||||| ||||| ||
gaaaaaagtattagaattttaattctttctctcctttttgcatcaaagtaggaaatacctgtttaatttctttcattttcatttttgctacttttcatagATCAGTAGTCAGAGATCAAAATGTCTCGAAGATATGACAGCCGTACAACAATCTTCTCCCCTGAAGGACGTCTTTACCAAGTGGAATATGCAATGGAGGC----------
upper sequence: AT4G15165.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv10s0042g00070.t01 (Vitis vinifera), 3'ss of exon 1
----------tttctttggaagctatataccca---taaacttaaaatgaata------aagatggaagctttagctgatataatttgggtgtttctttctttcttccttggtgtgaagC-TGTTTCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT
| | ||| | | ||| | | | |||| || || || | |||| ||| || ||| || | | | ||| || || | || || | |||||||||||||||||||||||| || || || ||||| || || ||||| ||||||||||| || || |||||
ctcatttgtctctgtttttgaatttcatatctaagttgtacttctttcttgtaccttctgagctgataacttt-gct-attccattgttgtactcttgacagACTTATTTCGTTTCCAGTGTGATACAAAATGTCTCGGAGGTATGATAGCCGTACAACAATCTTTTCCCCTGAAGGGCGTCTCTACCAAGTCGAGTATGCA------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaagctttagctgatataatttgggtgtttctttctttcttccttggtgtgaagCTGTTTCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT
agctgat putative branch site (score: 4)
tgtttctttctttctt putative PPT
tgatataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctttggaagctatatacccataaacttaaaatgaataaagatggaagctttagctgatataatttgggtgtttctttctttcttccttggtgtgaagCTGTTTCAAAATGTCTCGGAGGTATGATAGTCGCACCACGATCTTCTCACCGGAAGGTCGTCTCTACCAGGTTGAATATGCTATGGAAGCTATTGGCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - -cataaac
- - - - - - - - - - - - - - - - - -gaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatttgg