Sequence
atgc intronic sequence ATGC exonic sequence...aaaaaaacagagtaggttcctcgtccctttagctttaacacatgagctcttacaatgcggagtttctattgttgtaactgattgtttctccctggaatagATGGCATGCAGTTGCTTCATGGACATGGGATGCTCAAGACGAAACATGTGGGATATGTCGGATGGCTTTTGATGGTTGTTGTCCTGATTGCAAACTTCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05870.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05870.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G162356_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------------------------------aaaaaaacaga--gtaggttcctcgtccctttagctttaacacatgagctcttacaatg--cggagtttctattgtt-gtaactgattgtttctc---------cctggaa-----------tagATGGCATGCAGTTGCTTCATGGACATGGGATGCTCAAGACGAAACATGTGGGATATGTCGGATGGCTTTTGATGGTTGTTGTCCTGATTGCAAACTTCCT
| |||| | || || || || | | | | || |||| | || || | ||| ||||| || | ||| | | || | | ||||||||||| ||||| ||||| |||||||| || || || |||||||| ||||| |||||||||||||
gtaagagtcactctgcagtaatatgttaaagcccaaatatctcattctcttcatcagttgattgaggatttcttttctgcgtagtggactactaattcaaactgcccatacattacttgttcaatggattctg-catatgacaagatgcagtgaataaaacgtctcttgtttatatattgttgcattccagGTAGCACTATGAAGGTCAAGATTCTTCAGTGGCATGCAGTGGCTTCTTGGACGTGGGATGCACAGGATGAGACATGTGGCATATGCAGGATGGCTTTTGA----------------------------
upper sequence: AT3G05870.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G28310.1 (Glycine max), 3'ss of exon 1
aaaaaaacagagtaggttcctcgtccctttagctttaa------cacatgagctcttacaatgcggagtttctattgttgtaactgattgtttctccctgga-atagATGGCATGCAGTTGCTTCATGGACATGGGATGCTCAAGACGAAACATGTGGGATATGTCGGATGGCTTTTGATGGTTGTTGTCCTGATTGCAAACTTCCT
| || | | | | ||| || | || || | || | || | | | || ||| | | | ||||||||||||| |||||||||||||| |||||||| || || ||||| |||||||| ||| ||||||| |||||||| ||||||||||| || |||||||||
-------ttttccaaatttttagcctccctagtttctatcttttcatttgctttgcgactaaatcaagcacatccttaattttctcattcccttttgtcaaatatagATGGCATGCTGTTGCTTCATGGACTTGGGATGCCCAGGATGAAACCTGTGGGATTTGTAGGATGGCCTTTGATGGATGTTGTCCTGACTGTAAACTTCCT
upper sequence: AT3G05870.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G34030.1 (Glycine max), 3'ss of exon 1
aaaaaaacagagtaggttcctcgtccctttag--ctttaacacatgagctcttacaatgcggagtttctattgttgtaactgattgtttctccctgga-atagATGGCATGCAGTTGCTTCATGGACATGGGATGCTCAAGACGAAACATGTGGGATATGTCGGATGGCTTTTGATGGTTGTTGTCCTGATTGCAAACTTCCT
|| | | || | | | ||| ||||| | | | | | || | | || | | | | || || | | | ||||||||||||| ||||||| ||||| |||||||| || |||||||| |||||||| ||| ||||||| |||||||| ||||||||||| || |||||||||
-aatttttattctgaattttcagcctccttaattctttatctattcatttgtaactaaaccaagaacatcctaattt--ttggttcccttttgtgaaatatagATGGCATGCTATTGCTTCTTGGACTTGGGATGCACAGGACGAAACGTGTGGGATTTGTAGGATGGCCTTTGATGGATGTTGTCCTGACTGTAAACTTCCT
upper sequence: AT3G05870.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0046g03770.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------------aaaaaaacagagtaggttcctcgtccctttagct-ttaacacatgagctcttacaatgcggagtttctattgttgtaac---tgattgtttctccctggaa------tagATGGCATGCAGTTGCTTCATGGACATGGGATGCTCAAGACGAAACATGTGGGATATGTCGGATGGCTTTTGATGGTTGTTGTCCTGATTGCAAACTTCCT
| || | | || || | || | | || || | | | | ||| ||| || || | |||||| | ||| || ||| |||||||| || || ||||||||||||||||| ||||| ||||| |||||||| ||| ||||||| ||||||||||||||||||||||| ||||| |||
gtttttatatctggtactcaataattatatctttaactagatttccttttttctatgaagaaaaata--ctcacaaccttcttggttgttgacctgcatatttagatgtttcattttttatatagtaagaagccataattgttgtactctgtaaaaattgtagGTGGCATGCTGTCGCATCATGGACATGGGATGCCCAAGATGAAACCTGTGGGATTTGTAGGATGGCATTTGATGGTTGTTGTCCTGATTGTAAACTCCCT
upper sequence: AT3G05870.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0060g00290.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------aaaaaaacagagtaggttcctcgtccctttagct-ttaacacatgagctcttacaatgcggagtttctattgttgtaac---tgattgtttctccctggaa------tagATGGCATGCAGTTGCTTCATGGACATGGGATGCTCAAGACGAAACATGTGGGATATGTCGGATGGCTTTTGATGGTTGTTGTCCTGATTGCAAACTTCCT
| || | | || || | || | | || || | | | | ||| ||| || || | |||||| | ||| || ||| |||||||| || || ||||||||||||||||| ||||| ||||| |||||||| ||| ||||||| ||||||||||||||||||||||| ||||| |||
gtttttatatctggtactcaataattatatctttgactagatttccttttttctatgaagaaaaata--ctcacaaccttcttggttgttgacctgcatatttagatgtttcattttttatatagtaagaagccataattgttgtactctgtaaaaattgtagGTGGCATGCTGTCGCATCATGGACATGGGATGCCCAAGATGAAACCTGTGGGATTTGTAGGATGGCATTTGATGGTTGTTGTCCTGATTGTAAACTCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcttacaatgcggagtttctattgttgtaactgattgtttctccctggaatagATGGCATGCAGTTGCTTCATGGACATGGGATGCTCAAGACGAAACATGTGGGATATGTCGGATGGCTTTTGATGGTTGTTGTCCTGATTGCAAACTTCCT
ttgtttctccct CT-rich tract
tttctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaaaacagagtaggttcctcgtccctttagctttaacacatgagctcttacaatgcggagtttctattgttgtaactgattgtttctccctggaatagATGGCATGCAGTTGCTTCATGGACATGGGATGCTCAAGACGAAACATGTGGGATATGTCGGATGGCTTTTGATGGTTGTTGTCCTGATTGCAAACTTCCT
-aaaaaac
- - - - - - - - - - - - - - - - - -taacaca
- - - - - - - - - - - - - - - - - - - - - - - - cttacaa