Sequence
atgc intronic sequence ATGC exonic sequence...tcaataactttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagccagtatattcttatttgaaactcccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43070.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
------tcaataactttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagccagtatattcttatttgaaactcccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG---
| || ||| ||| || | || | | || | || | | || || | ||| | ||| | || ||||||| | || || | | ||||||| | ||||||||||| |||| || ||||| ||||||||||| |||||||| ||||||||||| || ||||
ttgatatgtgtatcttcagttag--atctgtcctgtaagatataccttttatctattatgaagtgttatagtgttagata-tgattcta---tccatactgcacagGTTGCTCGTGGTGATAACT---CTGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
upper sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G082330_T01 (Zea mays), 3'ss of exon 10
---------tcaataactttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagccagtatattctta-tttgaaactcccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG---
|| | |||| || | ||| || | || | | || || | || | ||||| | |||| || | || ||||||| | || || | || ||||||| || ||||| ||||| |||||||| || || ||||||||||| |||||||||||||| ||||| || ||||
attacatatacagggaacttgaccagccaacatttgctttaccttc-tacccattgagtcctgattattcttgc---tgtattcatgctttggaaattactc------agGTTGCTCGTGGTGATAACA---CTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG
upper sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G53880.1 (Glycine max), 3'ss of exon 9
-tcaata-actttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagcc--agtatattcttatttgaaactcccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG
||| | | || | | | | || | || || || | | || ||| ||||| || | |||||| |||||||| | ||| |||| |||||| | ||||| ||||| | || ||||||| | |||||||| ||||| ||||||||||||||||| ||||
tctaatggattctgtgttaacatgtgtctttattaaaaaggaagagagaattctggttttttatagttttgtgatactcttacatggg----ctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG
upper sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G47600.2 (Glycine max), 3'ss of exon 9
tcaataactttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagccagtatattcttatttgaaactc-------ccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG
||| || || || || || | || | ||| || || |||||| | |||| | || | | || | |||||| |||||||| | ||| |||| ||| || | ||||| ||||| | || ||||||| | |||||||| ||||| ||||||||||||||||| ||||
--aatggattctgt--gttttctataatgctgctttattaa---aaaggaagagagaattctggtttttatagttttttcatactcttacatgggctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGAGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG
upper sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
-tcaataactttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagccagtatattcttatttgaaactcccttctttgt------agGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG
|| || | ||| | | | ||| || | ||| | | || | | | | | |||| | ||| | | ||||| ||||||| | || |||| ||| ||| || |||||||| ||||| | || ||||||| |||||||||||||||||||||||||| |||||||| ||||
ttctattaacacctata--aattcagaatgacaacctaaatattta--gattcaccacaattagacaaat---ttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agggcccagagaagctcagccagtatattcttatttgaaactcccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG
ctcccttctttgt CT-rich tract
tatattcttatttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaataactttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagccagtatattcttatttgaaactcccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG
-caataac
- - - - - - - - - - - - - - - - - - - - - - - - - -cagagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactccc