Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgtaattccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16780.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 12
----gtaaatgtaattccgctggagtccgt--tcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
||| ||| | | | ||| || | | |||| ||| | | | | ||| | | | | ||||||||||| |||||||| ||||| ||||| ||||| || ||||| |||||| | | |||||||||||||||| || || ||||| || || |||||||
gtgagtacatgca--tataattaagtttgtcatttttcttatgcctataaaagttaatgc-taacttctaatataatgttatgcagGACTACAACGAGAAGCCTGATTACGGTCGTTGTGTTGCAATTGTGGCATCTGCTTCCTTGAGGGAAATGATAAGGCCGGGGGCTTTAGCCATTATATCAC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G069410_T01 (Zea mays), 3'ss of exon 4
--gtaaatgtaattccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttg-aactttatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
| | | ||| | || ||| | | | | ||| | || | | | || || ||| ||| ||||||||||| |||||||| |||||||| || ||||| || ||||| |||||| || | ||||| ||||||||||| || |||||| | || || |||||||
gtgagtacatgattaccatgaagttc--ttcagtccttttatgcttggaaaagcagatgctaacatgtaacaatatcatccagGACTACAAAGAGAAGCCGGATTATGGACGCTGTGTTGCAATTGTGGCATCTGCATCCTTGAGAGAAATGATAAAGCCTGGAGCTCTAGCAATTATATCAC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 12
gtaaatgta--attccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttg-aactttatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
|| | || | ||| | || ||| | ||| |||||| || | | | || ||| ||| ||| ||||||||||| |||||||| |||||||| || |||||||| ||||| || ||| || | || || |||||||||||||| || ||| | || || |||||||
gtgagtgcatgattaccatgaagttc-ttcagttttatgcttggaaa----agctgatgctaacttgtaacaatatcatccagGACTACAAAGAGAAGCCCGATTATGGACGCTGTGTCGCAATTGTGGCCTCTGCATCCTTAAGAGAAATGATAAAACCTGGGGCTCTAGCAATTATATCAC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 12
gtaaatgtaattccgct--ggagtccgttcccttttatttttatttttttcatcgggtgtctttttgaactttatg----tcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
|| | | | | | | | | | | | ||| |||| | | | ||||| |||||| | |||||| ||||||||||| |||||||||||||| ||||| || ||||| |||||| | | || || || ||||||||||| || |||||||| || || ||||
gtgagtttgggtttgtaaagtaatattatgtatgccagtttaggttttgatcttctctctttttttcccttttatgcttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCGTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 11
gtaaatgtaattccgctggagtccgttccctttta---tttttatttttttcatcgggtgtctttttgaac-tttatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
|| | | | | | || | | | ||| ||||| | | || | | || || | | | |||||| ||||||||||| |||||||||||||| ||||| || ||||| |||||| | | || || || ||||||||||| || |||||||| || || ||||
gtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 12
--------gtaaatgtaattccgctggagtccgttccctttta---tttttatttttttcatcgggtgtctttttgaactt-tatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
|| | | | | | || | | | ||| ||||| | | || | | || || | | | |||||| ||||||||||| |||||||||||||| ||||| || ||||| |||||| | | || || || ||||||||||| || |||||||| || || ||||
gtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttttgacagGATTACAAGGAGAAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCTTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCAC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 12
---------------------gtaaatgtaattccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
| | | || | || | || ||| ||||||| || | ||| | | |||| | | | || ||||||||| || ||||| ||||| |||||||| ||||| |||||||| |||||| || || ||||||| ||||||||||| || ||||||||||| ||||||
gtgagtatgattctctatagcatttttatggtttatcatgaat--gtaggttttaatttttaattgatgcat--gaaattgttttaacatgtttgctacagGACTATAAAGAGAAACCAGACTATGGTCGTTGTGTTGCCATTGTAGCATCTGCATCTCTGAGGGAGATGATAAAACCCGGTGCTTTGGCTATTGTATCACMapped 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|164126329|gb|ES197996.1|ES197996EST: TTGAGAGGCCTGGCATAATG GACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCT
genomic: TTGAGAGGCCTGGCATAATGgtaaatgtaa ... tatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
ttttatttttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgtaattccgctggagtccgttcccttttatttttatttttttcatcgggtgtctttttgaactttatgtcacagGACTACAAGGAGAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT