Sequence
atgc intronic sequence ATGC exonic sequence...ttattaacagcatcctcaatatctttaaccattagtgcctgtgaaagaaaacttgatttctccaatctctaacagagttttgtacaattgattagttcagATACGGGTTTTATGGTGATGTCATTTCAGAAAGTGAAAAATATCGGTGGATGGGTCCCAAACGCTATGACTATGTTGGAACTAAGATATTCTTGAAGCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51290.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G14280.1 (Glycine max), 3'ss of exon 9
ttattaacagcatcctcaatatc-tttaaccattagtgcctgtgaaagaaaacttgatttctccaat-ctctaacagagttttgtacaattgattagttcagATACGGGTTTTATGGTGATGTCATTTCAGAAAGTGAAAAATATCGGTGGATGGGTCCCAAACGCTATGACTATGTTGGAACTAAGATATTCTTGAAGCAC
| | | | | || | | | | | | ||| || | || | | | | | || | | | | |||| || | | |||| ||||| ||||||||||||||||| |||| ||||| || ||||| ||||||||||||||||| ||||| || | |||||| | | |||| || |||||
-tgagacatgtactggtatagtcatcttgcgtatgctacatgttaatccttaattattatatagatttcttcagtattatatcctaca-ttattgacctcagGTACGGATTTTATGGTGATGTCATCACAGAGAGTGAGAAGTATCGCTGGATGGGTCCCAAACGTTATGATTACGCTGGAACAATGGTATTTTTAAAGCAT
upper sequence: AT5G51290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G47530.1 (Glycine max), 3'ss of exon 9
-----ttattaacagcatcctcaatatctttaacca-ttagtgcctgtgaaagaaaacttgatttctccaatctctaacagagttttgtacaattgattagttcagATACGGGTTTTATGGTGATGTCATTTCAGAAAGTGAAAAATATCGGTGGATGGGTCCCAAACGCTATGACTATGTTGGAACTAAGATATTCTTGAAGCAC
| | || | | | | | ||| | ||| | | || |||||||| | | | | || | | || | | |||| || || ||||||||||||||||| |||| ||||| || ||||| ||||||||||||||||| ||||| || | |||||| | | |||| || ||||||
aaggaatttgctttgctgctttgttttttgtaaatacttattttcagttaaagaaaattaacagtaactagaaacttgggaaaatgaatatactc------ctcagGTATGGATTTTATGGTGATGTCATCACAGAGAGTGAGAAGTATCGCTGGATGGGTCCCAAACGTTATGATTACGCTGGAACAATGGTATTTTTAAAGCAC
upper sequence: AT5G51290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv16s0013g01750.t01 (Vitis vinifera), 3'ss of exon 9
ttattaacagcatcctcaatatcttta-accattagtgcctgtgaaagaaaactt-------gatttctccaatctctaacagagttttgtacaattgattagttcagATACGGGTTTTATGGTGATGTCATTTCAGAAAGTGAAAAATATCGGTGGATGGGTCCCAAACGCTATGACTATGTTGGAACTAAGATATTCTTGAAGCAC
| | || || | | | | | || | || || || || || ||| | | | | ||| | | | | | |||| | | ||| || || |||||||| ||||||||| |||||||||||||||| || |||||||| ||||| |||||||| |||| ||||| || | || |||| |||
----tgaaagaattcctacttattggatgcctcttgtatatgctaatcaaggttttcttggagatgttttctttttctgatatgatat-gctcaatc---ttatacagGTATGGATTTTATGGAGATGTCATTACAGAAAGTGAAAAATACCGCTGGATGGGCCCCAAGCGCTATGATTATGCAGGAACAAAAGTGTTTTTGAGACACMapped 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|164134265|gb|EL981480.1|EL981480EST: TTATGCAGCCTCATTCGCTGG ATACGGGTTTTATGGTGATGTCATTTCAGAAAGTGAAAA-TATCGGTGGAT
genomic: TTATGCAGCCTCATTCGCTGGgtaatggact ... attagttcagATACGGGTTTTATGGTGATGTCATTTCAGAAAGTGAAAAATATCGGTGGAT
EST:
gi|164142908|gb|EL968655.1|EL968655EST: TTATGCAGCCTCATTCGCTGG ATACGGGTTTTATAGGTGATGTCATTTCAGAAAGTG-AAAATATCGGTGGA
genomic: TTATGCAGCCTCATTCGCTGGgtaatggact ... attagttcagATACGGGTTTTAT-GGTGATGTCATTTCAGAAAGTGAAAAATATCGGTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaaacttgatttctccaatctctaacagagttttgtacaattgattagttcagATACGGGTTTTATGGTGATGTCATTTCAGAAAGTGAAAAATATCGGTGGATGGGTCCCAAACGCTATGACTATGTTGGAACTAAGATATTCTTGAAGCAC
aattgatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattaacagcatcctcaatatctttaaccattagtgcctgtgaaagaaaacttgatttctccaatctctaacagagttttgtacaattgattagttcagATACGGGTTTTATGGTGATGTCATTTCAGAAAGTGAAAAATATCGGTGGATGGGTCCCAAACGCTATGACTATGTTGGAACTAAGATATTCTTGAAGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - -aacagca
- - - - - - tcctcaa
- - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacagag