Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgtttttcagcacttgttgatgcttgggctagcttccttctattttggtttatttacttgtatctgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G17130.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 2
---------------------gtaaatgtttttcagcacttgttgatgct-tgggctagcttccttctattttggtttatttacttgtatctgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAG
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tgaaggatgttttcttgattgtcacagagttttcagatcaagtttgtttgattaactaggaacttttgatttagcatgctcttgttttgtgtg-tttgtagGTCACGCCAAATCTTTATGGCAATCTGGTGGCTAACACGGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAG
upper sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 2
------------gtaaatgtttttcagcacttgttga-tgcttg--ggctagcttccttctattttggtttatttacttgtatc------tgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAG
| || ||| | || | || ||||| || | | || || |||| | || || | |||| |||| ||||||||||| ||||| ||| | ||||| ||||| ||||| ||||||| |||||| || || ||||||||||||
tcatcacatttcttttctgctttcctaattttctcgaatgcttctttgcaaatacaccatggattaggattatctgtgggtttcaatcttttttttgtagGTTACGCCTAATCTTTATGGCAATTTGGTGGCTAACACGGCTGCAGGTATTGTTGGAGGGACGGGCATCATGCCTGGAG
upper sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 2
-----------------gtaaatgtttttcagcacttgttgatgcttgggctagcttccttct---attttggttta-tttacttgtatctgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAG
| | | || ||| || ||| || | | | ||| || ||| ||| | |||| |||| || || ||||| ||||| ||||| ||||| || ||||| |||||||||||||| ||||| |||||||||||||
ttctaaagggctttttttccagaataatatgaagatttcaaatgatttaattagattacctgtggagtttgaacatacttttctttggttccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAG
upper sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G00500.1 (Glycine max), 3'ss of exon 1
gtaaat--gtttttcagcacttgttgatgcttgggctagcttccttctattttggtttatttacttgtatctgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAG
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gttagttagttaattggttactatagtatcatcttcccttccctttccaatctaaatctctt-ctcgtgttattatctcagGTGACTCCTAATCTCTATGGAAATCTAGTGGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAG
upper sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------gtaaatgttttt-cagcacttgttgatgcttgggctagcttccttctattttggtttatttacttgtatctgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAG
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gtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtt-tgccttggtgctattgtgtgtatttttcccccagGTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116429007|gb|EG471599.1|EG471599EST: ATAATTGTTGTATGCAACTTGTGGCTAGACCAGAGCAATTCGATGTCATG GTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATT
genomic: ATAATTGTTGTATGCAACTTGTGGCTAGACCAGAGCAATTCGATGTCATGgtaaatgttt ... tgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcttgggctagcttccttctattttggtttatttacttgtatctgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAG
tgttgat putative branch site (score: 4)
tctgcttt putative PPT
tattttggtttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgtttttcagcacttgttgatgcttgggctagcttccttctattttggtttatttacttgtatctgctttgcagGTGACGCCTAATCTCTATGGTAATCTAGTGGCAAACACTGCTGCTGGTATTGCTGGAGGTACTGGAGTCATGCCTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG