Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttagaattcgttctatggcttagggttttagtgttcgaaattgagatttaaaaagggatttgttctaaggcttagggtttgtacttaccacattctgcttttggttactgtttggcagACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19910.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g41450.1 (Oryza sativa), 3'ss of exon 2
gtaagtttagaattcgttctatggcttagggttttagtgttcgaaattgagat-ttaaaaagggatttgttctaaggcttagggtttgtacttaccacattctgcttttggttactgtttggcagACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTAT
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-----------------------gcttctgctatttttaatggaatcaaacttgttaaatgagtactgaaattaatact--gtatgtaaaatggcatttggctaatatttcttatgttgaaacagATCTAGCACAGAATAGGTACTTTGAGGATGAGGCATTTATCGGGTATCTCAAGTATCTCAAATACTGGCAGCGTCCGGAGTACATCAAATACATAAT
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G139683_T03 (Zea mays), 3'ss of exon 2
gtaagtttagaattcgttctatggcttagggttttagtgttcgaaattgagatttaaaaagggatttgttctaaggcttagggtttgtacttaccacattctgcttttggttactgtttggcagACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTAT
| |||||| ||||| | | ||| || || || || | | || | | | || | ||| ||| | ||| || || |||||| | ||||| || ||||| |||||||| || ||| | |||||||| |||||||||||||||||||||| ||||| | ||| ||
---------------gcctcatggctccttgttttt-tacttgaactttcttgttcaatgcacatcatgtttggtact--gcatggatgatttgaatgctctttcttttccca------aatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G28990.1 (Glycine max), 3'ss of exon 2
gtaagtttagaattcgttctatggcttagggttttagtgttcgaaattgagatttaaaaagggatttgttctaaggcttagggtttgtacttaccacattctgcttttggt-tactgtttggcagACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTAT
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-------------atgagccatgctttgtcatttcaatgt--gtatctgagttacttttatagttttgttt----------gttttttttttaccttattcttatattgttacacttttgaacagATTTGGCTCAGAATCGATACTTTGAGGATGAAGCATTCATTGGATACTTAAAGTATCTTCAATATTGGCAACGCCCTGAATATATTAAATTTATTAT
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G38750.2 (Glycine max), 3'ss of exon 3
gtaagtttagaattcgttctatggcttagggttttagtgttcgaaattgagatttaaaaagggatttgttctaaggcttagggtttgtacttaccacattctgcttttggttac--tgtttggcagACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTAT
| || | | | | ||| |||| || | || || || || ||| | || || ||||| | || ||||| | || |||| |||| || ||||| || ||||| ||||||||||| ||||||||||| |||||||||||||| ||||| || || || || || || || |||||
---------------------tttttttaaaatgcaccatgct---ttgtcatttgaatgtgtatctgagttac--ttttatatttttttttgccttattcttatatttgttacacttttgaacagATTTGGCCCAAAATCGATACTTTGAGGATGAAGCATTCATTGGATACTTAAAGTATCTTCAATATTGGCAACGCCCTGAATATATTAAATTTATTAT
upper sequence: AT5G19910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0039g02760.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtttagaattcgttctatggcttagggttttagtgttcgaaattgagatttaaaaagggatttgttctaaggcttagggtttgtacttaccacatt--ctgcttttggttactgtttggcagACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTAT
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-------------------agtgcaaaaaaaatttagtgtt--gaattcacttctttggtgtcattaatt-----gtttagtctctgtttcttccctgatgattgcttattgaattttttactcagATTTGGCTCAAAATCGCTATTTTGAAGATGAAGCTTTCATTGGCTACTTGAAATACCTTCAATATTGGCAACAACCAGAGTACATAAAATTCATAATMapped 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|86059929|gb|DR355686.1|DR355686EST: ACTGGAACTTGAATTTATTCAATGTCTCGCCAATCCTACTTACATCCACT ACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGA
genomic: ACTGGAACTTGAATTTATTCAATGTCTCGCCAATCCTACTTACATCCACTgtaagtttag ... tgtttggcagACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaaggcttagggtttgtacttaccacattctgcttttggttactgtttggcagACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTAT
tacttac putative branch site (score: 1)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttagaattcgttctatggcttagggttttagtgttcgaaattgagatttaaaaagggatttgttctaaggcttagggtttgtacttaccacattctgcttttggttactgtttggcagACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG