Sequence
atgc intronic sequence ATGC exonic sequencegtactaatcatctaatttaccttgctacttcttcacaccaccacatgcgtcttataacatttctaatgtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28900.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
gtactaatcatctaatttaccttgctacttcttcacaccaccac-atgcgtctta-taacatttctaat-gtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA
| |||| | | || | | | ||| | | ||| | ||||| | || || ||||| || || || || || || || || ||||| || || |||||||||||||||||||| | || ||||||||||||| ||||||||| || |||||||
---gtgatca-caacttcttgccataaagcagtgaattcactgttaatcatctaaataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
gtactaatcatc--taatttaccttgctacttcttcacaccaccacatgcgtcttataacatttctaatgtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA
|| | || ||| |||| || || | || | | | | || |||| | ||||||| || | |||| || || || || || | || || |||||||| |||||||||||||| |||||||| | || ||||||||||||| ||| ||||| || |||||||
gtgattataatccttaataaactttagatttgctgccaagtattaa----gttaaataat-tggctaatgtttaattg---tagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 11
-----------------------gtactaatcatctaatttaccttgctacttcttcacaccaccacatgcgtcttataacatttcta---atgtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA
|| | | | ||| || || | || | | || | ||| || || || | || |||| || |||||||| ||||||||||| ||||| || ||||| ||| |||| ||||||||||| ||||||||||||||||| |||||||| ||||||||||
gtgcatgaaatatttgataaaatttattgcattcttgagttagtatg-tatgcttggctactgttagtgacttccttggtaattggtatgcatatcttgtgtgaatagGAACGTGAGAACCCAACATTGACAGAGTGGGATCGATTTGCTCATCGAGAATATATTAGGCTTTCAATGGAAGAAGATGTAGAAGATGCCTCTAATGGAA
upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
gtac-taatcatctaat-------ttaccttgctacttcttcac--------accaccacatgcgtcttataacatttcta----atgtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA
|| | | | || | || ||| |||| | ||| || | | || | || | ||||| | ||||||| || ||||| |||||||||||||| ||||| || ||||| |||||||| ||||||||||| || |||||||||||||| || ||||| ||||| || |
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 11
-------------------gtactaatcatctaatttacct--tgctacttcttcac-accaccacatgcgtcttataacatttcta---atgtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA
| | || | || | | | | | ||| | || | | || | ||| || ||||| || || |||| || |||||||| ||||||||||| ||||| || ||||| ||| |||| ||||||||||| |||||||||||||| | |||||||| ||||| ||||
gtgcatgaaatatttgataaaatttattgcattgttgagttagtatttatgcttggctactgttagtgacttccttggtaattggtatgcatgtcttgtgggaatagGAACGTGAGAACCCAACATTGACAGAGTGGGATCGATTTGCTCATCGAGAATATATTAGGCTTTCAATGGAAGAAGACATAGAAGATGCCTCTAACGGAAMapped 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|124943855|gb|EL020008.1|EL020008EST: TCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAG GAGCGAGAGAACCCTACATTGA
genomic: TCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAGgtactaatca ... acggaaacagGAGCGAGAGAACCCTACATTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcttcacaccaccacatgcgtcttataacatttctaatgtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA
ttctaat putative branch site (score: 2)
ttataacatttctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaatcatctaatttaccttgctacttcttcacaccaccacatgcgtcttataacatttctaatgtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG