Sequence
atgc intronic sequence ATGC exonic sequence...gacattgtttagtgaatgggaaaaaaggaatcatttttgcgtttttgattctgaaatgtttgattgtgaatctgattttatactgttttcttacctgtagGCTGTTTGCATACCGTCTATATTGTCTGGGAAAGATGTGATTGTTGCAGCAGAAACTGGTAGTGGTAAAACACATGGTTATCTTGCTCCAATAATTGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G59990.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G59990.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os09g21520.1 (Oryza sativa), 3'ss of exon 1
gacattgtttagtgaatgggaaaaaaggaatcatttttgcgtttttgattctgaaatgtttgattgtgaatctgattttatactgttt-tcttacctgtagGCTGTTTGCATACCGTCTATATTGTCTGGGAAAGATGTGATTGTTGCAGCAGAAACTGGTAGTGGTAAAACACATGGTTATCTTGCTCCAATAATTGATC
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tactctttctaggacctatgtgccattagag-atttatatatgtatttttctaattgccctcaaaatagtacttacggattacttcaaatgctgaatgcagGCAGCCTGTATACCACACGTTCTCACAACAAACGATGTAATTGTTGCTGCTGAGACTGGGAGTGGCAAAACACATGGTTACCTTGTTCCATTGATTGAAA
upper sequence: AT1G59990.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G100043_T01 (Zea mays), 3'ss of exon 1
gacattgtttagtgaatgggaaaaaaggaatcatttt-tgcgtttttgattctgaaatgtt-tgattgtgaatctgattttatactgttttcttacctgtagGCTGTTTGCATACCGTCTATATTGTCTGGGAAAGATGTGATTGTTGCAGCAGAAACTGGTAGTGGTAAAACACATGGTTATCTTGCTCCAATAATTGATC
|| | ||| || | | | ||| | || | | | | | | ||| || ||| | || | | | || || |||| || ||||| | | | | || ||||| ||||| |||||||| ||||||||||| ||||| |||||||| |||| || | |||||
-actatatttc-cagatatgtatatcctaattgtcttgttcagtgcctactgttgcatgcaactatgaaaaatactaacataaagtttcaaattttatgcagGCAACCTGTATACCACATGTTCTCATGGCAAATGATGTAATTGTCGCAGCAGAGACTGGTAGTGGCAAAACCCATGGTTACCTTGTACCTTTGATTGAAA
upper sequence: AT1G59990.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0026g00640.t01 (Vitis vinifera), 3'ss of exon 1
gacattgtttagtgaatgggaaaaaaggaatcatttttgcgtt-tttgattctgaaatgtttgattgtgaatctgattttatactgttttcttacctgtagGCTGTTTGCATACCGTCTATATTGTCTGGGAAAGATGTGATTGTTGCAGCAGAAACTGGTAGTGGTAAAACACATGGTTATCTTGCTCCAATAATTGATC
|| | | | | || ||| | ||| | || || || ||| || || | ||| | ||| | | | | | ||||||| ||| ||||| | |||| | || || || |||||| | ||||||||||| ||||||||||||||||| ||||| || | | |||| ||||||||
-gttttctattgggcttgttaaatagaaggccatgataaatttactttcttttgagattttgctgtatgataattattgagatatttgatttgcattctagGCTGCTTGTATACCCTATATACTTTCAGGCAATGATGTGGTAGTTGCAGCAGAGACTGGTAGTGGTAAAACGCATGGCTACTTAGTTCCACTAATTGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattctgaaatgtttgattgtgaatctgattttatactgttttcttacctgtagGCTGTTTGCATACCGTCTATATTGTCTGGGAAAGATGTGATTGTTGCAGCAGAAACTGGTAGTGGTAAAACACATGGTTATCTTGCTCCAATAATTGATC
ttcttac putative branch site (score: 2)
ctgttttcttacct CT-rich tract
attttatactgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacattgtttagtgaatgggaaaaaaggaatcatttttgcgtttttgattctgaaatgtttgattgtgaatctgattttatactgttttcttacctgtagGCTGTTTGCATACCGTCTATATTGTCTGGGAAAGATGTGATTGTTGCAGCAGAAACTGGTAGTGGTAAAACACATGGTTATCTTGCTCCAATAATTGATC
- - -tgtttag
- - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - - - gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - - ctgaaat