Sequence
atgc intronic sequence ATGC exonic sequencegtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G17130.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA------------
|| | |||| || || || | ||| | || | | || | | | ||| ||| | || |||| |||| ||||| ||||||| |||||||| || || ||| | ||||| || ||||| ||||||||||| ||| | |||||| | |||||||| ||||||||||| || || || |
--------------------------------attgccaatggaatgaaatgcacccttttttttttccagttctctgagcttct--tttccatctta--------gtctcactga--ctaac-ttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG
upper sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
||| | || || | |||| || || || | ||| | || | | || | | | ||| ||| | || |||| |||| ||||| ||||||| |||||||| || || ||| | ||||| || ||||| ||||||||||| ||| | |||||| | |||||||| ||||||||||| || || || |
--------------------ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttct--tttccatctta--------gtctcactga--ctaac-ttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
upper sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 1
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
||| | | | | | |||||| ||| | | | |||| | | | ||| || | | || | || ||| || | | | ||| |||||||| ||||||||||| || || | ||||| |||||||| |||||||| || ||| | |||||||| |||||||| || || ||||| || || || |
----------------tttctgaaatagaacgtatgtaaatgt--ttttgtcacttttcatttcatcatctaaaggaatttt-----tttctatatggtac------tgttactaa----atggatttactagGTGATCACAAAGTTCTGCTCTGAAAGGATTGCCAAGTATGCTTTTGAGTACGCGTACCTCAACAACAGAAAGAAAGTGACTGCCGTGCATAAAGCAAACA
upper sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 1
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
| |||| ||| || ||| | | ||| | | | || || || | | ||| | | || | | | || |||| |||||||| ||||| ||||| || || | |||||||||||||| ||||||||||| ||| | ||||| | |||||||| ||||||||||| || || ||||
-------------------------taatttgaaagtgcatgcaat---attgctgctcctttctattttgccatctaaa----aggcatttctcct-tattactatttactataactttgttgatttgctagGTGATAACAAAATTCTGCTCTGAAAGAATTGCAAAGTATGCTTTTGAGTATGCATACCTTAACAATCGAAAGAAAGTGACAGCAGTGCATAAAGCCAATA
upper sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttat-atcaaagatgtctctgatgct----aatgtt----ttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
| || | || ||| || | || | | | || | | | || | ||||| ||||| ||||| | |||| || ||||||| || || ||||| || ||||| ||||||||||| || ||||||||||| || | |||||| | |||| ||| |||||||| || ||||| || |
-----------------------------------------gcgactctatgtatattg-cataatacctgtcgaatgacctgctggtttctgccttgttgtcaaatatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA
upper sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtag-atgtgaaagttggagatgttcatgttatatcaaagatgtctc-tgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
| | | || || ||| ||| || | || | ||| ||| | || | || || ||| || | || |||| || || |||||||| || ||||| ||||| || || || ||||||||||| || | |||||| | |||| ||| ||||||||||||||||| || |
-------------------------------atctcctcgtcatgcttcatgcattgtgga--aataatcttatctactgcgtggtacctgtcaaataattctgtaagtgccttacagtgccaagatgtt--cagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTATGCTTATCTCAACAACCGCAAGACAGTAACAGCAGTGCACAAGGCCAACA
upper sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgtt-catgttatatcaaagatgtctctgatgctaatgtt-ttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
| | | | | |||| ||| | || | ||| || | | || | | | || | || | || ||| | ||| ||||||||||||| ||||| || ||||| || ||||| ||||| ||||| ||||| || | |||||| | |||| |||||||||||||||||||| || |
---------------------------------caagagggcttgtcagtgtcat-gtg-tatgatcgtatctgcaggtttcctacttgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA
upper sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ13705 (Selaginella moellendorffii), 3'ss of exon 1
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
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-------------------------------------------------------------gtactccaatttcttctcctctgctttgctcg-gccgctccagctacgtttc---ttcttgcgcac---cagGTGATCACGAAGTTTTGCTCCGAACGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA
upper sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
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-------------------------------------------------------------gtactccaatttcttctcctctgctttgctcg-gccgctccagctacgtttc---ttcttgcgcac---cagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACAMapped 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|116428995|gb|EG471587.1|EG471587EST: ATGCAGGTCTTGAACATGAAGTTGTTCCTGGTGTTGTTGAGAGCCTTAAG GTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTAT
genomic: ATGCAGGTCTTGAACATGAAGTTGTTCCTGGTGTTGTTGAGAGCCTTAAGgtgcaatttc ... gttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTAT
EST:
gi|116429007|gb|EG471599.1|EG471599EST: ATGCAGGTCTTGAACATGAAGTTGTTCCTGGTGTTGTTGAGAGCCTTAAG GTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTAT
genomic: ATGCAGGTCTTGAACATGAAGTTGTTCCTGGTGTTGTTGAGAGCCTTAAGgtgcaatttc ... gttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
tgctaat putative branch site (score: 2)
ttatatcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA