Sequence
atgc intronic sequence ATGC exonic sequencegtagtattttttatttcattagattgtagttcatgattcttgatctctttatctgtctcctgtcaccgattcgatagtaaattaggattcatcggtattccactgtggagaataaatgttagaaacttttcatttcagATAATGAGAGATCCCGATACTGGAAACTCACGAGGTTTTGGTTTCATCAGCTATGACTCCTTTGAAGCATCTGATGCTGCTATTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18510.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 3'ss of exon 6
gtagtattttttatttcattagattgtagttcatgattcttgatctctttatctgtctcctgtcaccgattcgatagtaaattaggattcatcggtattccactgtggagaataaatgttagaaacttttcatttcagATAATGAGAGATCCCGATACTGGAAACTCACGAGGTTTTGGTTTCATCAGCTATGACTCCTTTGAAGCATCTGATGCTGCTATTGAG
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-----------------------------------aacatgtactacttcaatcgtttaccat-gcagtgttaatagtgtatttccagt-gttggcatacagtaattt-gctttgattttttttatttatctttatagATAATGCGAGATCCTGAAACTGGAAATTCACGAGGCTTTGGCTTTGTGAGCTATGACTCCTTTGAATCATCTGATCAAGCTATAGAG
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 6
gtagtattttttatttcattagattgtagttcatgattcttgatctctttatctgtctcctgtcaccgattcgatagtaaattaggattcatcggtattccactgtggagaataaatgttagaaacttttcatttcagATAATGAGAGATCCCGATACTGGAAACTCACGAGGTTTTGGTTTCATCAGCTATGACTCCTTTGAAGCATCTGATGCTGCTATTGAG
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--------------------ggtatcaagccaatgacaattaaaaa---taaccaccacctgaaag-gattcatt--tcactcaacatt-atgtatat-----------gatctgatattcaaggctttttgttgcagATCATGAGAGATCCTGAGACAGGAAATTCCCGTGGTTTTGGCTTCATTAGCTATGATTCATTTGAGGCATCTGATTCAGCCATTGAG
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 6
gtagtattttttatttcattagattgtagttcatgattcttgatctctttatctgtctcctgtcaccgattcgatagtaaattaggattcatcggtattc---cactgtgga---gaataaatgttagaaacttttcatttcagATAATGAGAGATCCCGATACTGGAAACTCACGAGGTTTTGGTTTCATCAGCTATGACTCCTTTGAAGCATCTGATGCTGCTATTGAG
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----------------------------------------tagtctcttgttctttaaac-acaacccccccatacctgaa--aggattcattt-tattcaaacattatgtatatgatctaacatacaaggctttgtgttgcagATCATGAGAGATCCTGACACAGGAAATTCCCGTGGTTTTGGCTTCATTAGCTACGATTCATTTGAGGCATCTGATTCAGCCATTGAG
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 6
gtagtattttttatttcattagattgtagttcatgattcttgatctctttatctgtctcctgtcaccgattcgatagtaaattaggattcatcggtattccactgtggagaataaatgttagaaacttttcatttcagATAATGAGAGATCCCGATACTGGAAACTCACGAGGTTTTGGTTTCATCAGCTATGACTCCTTTGAAGCATCTGATGCTGCTATTGAG
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--------------------------ttaaaaatgcacagggacaatttcatttgtgttctgt-gctgact------aaaatgatgatgcttc-----tttgcaattgaatatgacgtttggcacttctccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S70_254V6.1 (Physcomitrella patens), 3'ss of exon 6
------gtagtattttttatttcattagattgtagttcatgattcttgatctctttatctgtctcctgtcaccgattcgatagtaaattagg-attcatc-ggtattccactgtggagaataaatgt--------tagaaacttttcat----ttcagATAATGAGAGATCCCGATACTGGAAACTCACGAGGTTTTGGTTTCATCAGCTATGACTCCTTTGAAGCATCTGATGCTGCTATTGAG
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gtatggttatcatcttgcgtttgtgggggtttggatgtgtagtctgcgcgcttgttcgctcccctaagtaattttgaggtttttagactatgtatttatccagtaataagataaggataaaaaacgtactgccgattcaaaattttggtggaattcagATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCAGCTACGATTCGTTTGAAGCTTCAGACTCTGCAATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggattcatcggtattccactgtggagaataaatgttagaaacttttcatttcagATAATGAGAGATCCCGATACTGGAAACTCACGAGGTTTTGGTTTCATCAGCTATGACTCCTTTGAAGCATCTGATGCTGCTATTGAG
cttttcatttc CT-rich tract
aataaatgttagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtattttttatttcattagattgtagttcatgattcttgatctctttatctgtctcctgtcaccgattcgatagtaaattaggattcatcggtattccactgtggagaataaatgttagaaacttttcatttcagATAATGAGAGATCCCGATACTGGAAACTCACGAGGTTTTGGTTTCATCAGCTATGACTCCTTTGAAGCATCTGATGCTGCTATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT