Sequence
atgc intronic sequence ATGC exonic sequence...gatgattttttctgccatctgttatatgatccgcgtaagatgaacatactataaacgaaaagccttgggttaacaatccaacattaactgagatttgtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAAGGCAGTGGGCACCCGTTTTTAGTGAACTTCCTCTTGGTCCGCAACGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G24290.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g07194.1 (Oryza sativa), 3'ss of exon 6
-gatgattttttctgccatctgttatatgatccgcgtaagatgaacatactataaacgaaaagccttgggttaacaatccaacattaactgagatttgt--agATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAAGGCAGTGGGCACCCGTTTTTAGTGAACTTCCTCTTGGTCCGCAACGAAA
| | | | | | || | | | || | || | || |||| | | ||| | |||| | || | ||| ||||||||| | ||||||||||||||| || ||| | ||||| ||||| |||||||||||||| || |||| ||||| || ||||||||||| || | ||
tcgtatcatggcatacagacaatcattctagctaggaaaaa-gatggcattaggcctgaaacaacacaagc-aactgtgtgacatgtg-taagttctgtgcagATAAGCCTCAAATTGAAGAGCTGCACCAATTTTTGGAGTTCCAGCTTCCAAGGCAGTGGGCTCCTGTTTACAGTGACCTCCCTCTTGGTCCTCAGAGGAA
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g72860.1 (Oryza sativa), 3'ss of exon 5
------gatgattttttctgccatctgttatatgatccgcgtaagatgaacatactataaacgaaaagccttgggttaacaatccaacattaactgagatttgtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAAGGCAGTGGGCACCCGTTTTTAGTGAACTTCCTCTTGGTCCGCAACGAAA
|| | || | | | | | | | ||| | | | || | || | | | | | | || ||| || ||||||||| | | |||| || |||| |||||| | ||||||||||| ||||||||||||||||| || | ||||| || ||||| ||||| || | ||
cacaaacataagaattctagttagcaaacagtggcattgggccagagaattgaa--agcaatgttaaacagttaggtgataccttttttttttctgg----tgcagATAAGCCGCGAGTTGAGGAATTGCACCAGTTTTTAGAGTTTCAGCTTCCAAGGCAGTGGGCACCTGTCTACAGTGACCTCCCTCTGGGTCCTCAGAGGAA
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G435034_T01 (Zea mays), 3'ss of exon 4
gatgattttttctgccatctgttatatgatccgcgtaagatgaacatactataaacgaaaagccttgggttaacaatccaacatta-actgagattt---gtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAAGGCAGTGGGCACCCGTTTTTAGTGAACTTCCTCTTGGTCCGCAACGAAA
| || | | || || | | | | ||| || || | ||| | ||||| | || | ||| |||| | |||||| || ||||| || || | ||||||||| | ||||| ||||| ||||||||||||||||| |||| ||||| || |||| ||||| || | ||
----acttatggttgcaacttgcaaagcacacaatctagaaaaattagtattatgccgcaagtccaattgcaacaacctggtgatatattgaaatttggtgcagATAAACCTCCAATCGAGGAATTACATCAGTTTTTGGAGTTCCAGCTTCCAAGGCAGTGGGCACCTGTTTACAGTGATCTCGCTCTGGGTCCTCAGAGGAA
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G28780.1 (Glycine max), 3'ss of exon 6
gatgattttttctgccatctgttatatgatccgcgtaagatgaacatactataaacgaaaagccttgggttaacaatccaacattaactgagatttgtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAAGGCAGTGGGCACCCGTTTTTAGTGAACTTCCTCTTGGTCCGCAACGAAA
||| ||| || | |||| || | | || | ||| || | | || | || || ||| | || | |||||| ||||| |||| |||||| || || || | || || ||||| ||||||||||||||||| || || ||||| |||||||||||||| ||||||||
-gtgagaaaaattgctattt-ttatttg-catacattctatctaaataacatttccctttggtatttgacta-----taaaaattgtccattat--gcagATAAACCACCGATTGTAGAGCTCCACCAATTCTTGGAATTCCAGCTGCCAAGGCAGTGGGCACCTGTATTCAGTGACCTTCCTCTTGGTCCCCAACGAAA
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 4
gatgattttttctgccatctgttatatgatccgcgtaagatgaacatactataaacgaaaagccttgggtta--acaatccaacattaactgagatttgtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAAGGCAGTGGGCACCCGTTTTTAGTGAACTTCCTCTTGGTCCGCAACGAAA
||| ||| || | |||| || | | || | ||| || | | || | || ||||| ||||| || |||||| ||||| ||||||||||| || || || | || || ||||| ||||||||||||||||| || || ||||| |||||||||||||| ||||| ||
-gtgagcaaaattgctattt-ttatttg-catacatcctatctaaataacatttcctttcggtatttgtctataacaattgtccatta---------tgcagATAAACCACCGATTGAAGAGCTCCACCAATTCTTGGAATTCCAGCTGCCAAGGCAGTGGGCACCTGTATTCAGTGACCTTCCTCTTGGTCCACAACGGAA
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv12s0035g01040.t01 (Vitis vinifera), 3'ss of exon 6
gatgattttttctgccatctgttatatgatccgcgtaagatgaacatactataaacgaaaagccttgggttaacaatcc--aacattaac-tgagatttgtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAAGGCAGTGGGCACCCGTTTTTAGTGAACTTCCTCTTGGTCCGCAACGAAA
|| | | || | | | || | | || | | ||| ||| |||| ||| |||||| | | ||| |||||| ||||| |||||||| || | |||||| | || ||||| || ||||||||||||||||| || || |||||||||||||||||||| ||| | |
-gtg-tagaaaaaggcagcgttcacattcttt-tgcttattgctgctgaatcggtcaaaatcatttgaactaaccatctgtaacattttcattgtccttgcagATAAACCACCCATTGAAGAACTACGCCAGTTTTTGGAATTTCAACTGCCAAGGCAGTGGGCACCAGTGTTCAGTGAACTTCCTCTTGGTCCACAAAGGAGMapped 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|86067785|gb|DR363542.1|DR363542EST: AGTTCCAGGAAGTGGATTCTTAAGCCATGCCATAAATCTGTATCTAAGAT ATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAA
genomic: AGTTCCAGGAAGTGGATTCTTAAGCCATGCCATAAATCTGTATCTAAGATgtaagcctat ... agatttgtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAA
EST:
gi|86067783|gb|DR363540.1|DR363540EST: AGTTCCAGGAAGTGGATTCTTAAGCCATGCCATAAATCTGTATCTAAGAT ATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAA
genomic: AGTTCCAGGAAGTGGATTCTTAAGCCATGCCATAAATCTGTATCTAAGATgtaagcctat ... agatttgtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atactataaacgaaaagccttgggttaacaatccaacattaactgagatttgtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAAGGCAGTGGGCACCCGTTTTTAGTGAACTTCCTCTTGGTCCGCAACGAAA
cattaac putative branch site (score: 2)
ttaacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgattttttctgccatctgttatatgatccgcgtaagatgaacatactataaacgaaaagccttgggttaacaatccaacattaactgagatttgtagATAAGCCACCAATTGAAGAGCTGCATCAGTTTCTCGAGTTTCAGCTACCAAGGCAGTGGGCACCCGTTTTTAGTGAACTTCCTCTTGGTCCGCAACGAAA
- - - - - - - - - - - - - - - - - - - - - aacatac
- - - - - - - - - - - - - - - - - - - - - - - - - - -aacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatccaa