Sequence
atgc intronic sequence ATGC exonic sequencegtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G29160.3 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 9
gtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC
|| || |||| || || || | ||| || | || || || || || || | |||| || || | | || ||||||||| || ||||| || ||||| || | ||||||| | |||||||| ||||| || ||||| || |||||||||||||| || || |||||||||||
------------------------------------------gtttt----atgctgt-tactataaggt-tct-tatttattcactttatttattataagttatcctaattcatttgtctgtatttatttaacagTCTCGAGCACATCCACGAGAAATAATAACTGAAGTTCTTAAAGCTCTGCAAGAGCTAAATGTTTGCTGGAAGAAGATTGGACATTATAACATGAAATGCA
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 9
gtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC
| | |||| || | ||| || ||| | | | | | || | || ||||| | |||| | ||||||||| || ||||| || ||||| || | |||||| | |||||||| |||||||| ||||| | ||||| |||||||| |||||||||||||||||
---------------------------------------gtaattttct---tgttaagtacatcttatgatgtgtttcatgaattattccgaattccgat---tcatttatctgtaa-----ttgtct--aacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAAGAACTGAATGTTTACTGGAAAAAGATTGGACACTACAACATGAAATGCA
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 10
gtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC
| || | | || | | || | | |||| |||| ||| | | | | | | || ||| ||||| |||||||| || |||||||||||||| |||| ||| ||| | |||||| | |||||| | ||||| |||||||||||||||||||||||||||||||| |||
---------------------------atatctaaaagctgtttgtttttgtaatagtggccatcagaaaaattgtagtcttgatgtcttgttggt--agttacttactttttgtttatcttgt-------gacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTTCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 9
gtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttg-aacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC
| | | || || | | || | | |||| | || ||| | | | ||| | || |||| || | ||| |||||||| || |||||||||||||| |||| ||| || | |||||| | |||||| | ||||| |||||||||||||||||||||||||||||||| |||
-----------------------------taacggctgtttgaatttttgta-atagttgccatcagaaaaattgtagttttgatgtcttgttggt---agttatatactttttgtt----cattatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
gtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctt-tgcctctacatagccaaa-tcgataatcattctgttaccttgttgttttg-aacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC
|| || || | | | | || ||| | || | | || | | | | || | | || |||| |||| ||| | |||||| || || || |||||||| |||| ||| || | |||||||| |||||| | ||||| ||||||||||||||||| ||||| |||||||| ||
-----------------------------------ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtt----tgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
gtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC
|||| || || | | | | | | || | || | |||| ||| || || | | | || || || | | | || | || |||||||| || || ||| | | || |||| ||||||| | |||||||| |||||||| |||||||||||||| |||||||| || ||||||||||||||
------------------------------gctcatcaaaatattatttacaatcttc-tttgattatat-cttatactgttttgct-tataagaaaagaataatgattatcttttcaactaactttt---gacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCAMapped 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|47832194|gb|CK121878.1|CK121878EST: GAGCAAGATCACAAGTCCCTGTTGATCGAAAATGGGCTCTTGGACTTCAG TCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAA
genomic: GAGCAAGATCACAAGTCCCTGTTGATCGAAAATGGGCTCTTGGACTTCAGgtttgttcct ... ttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC
ttgtttt CT-rich tract
ataatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG