Sequence
atgc intronic sequence ATGC exonic sequencegttggggttctcttctgatgtcaagattcttcgctttggtagaagttagttagtttctcatatcttgttctaatgatttttggcagATACATGATGAGGCTAAAAAGTTCTCTTACCAAACTGGTGTGAAGGTGGTTGTTGCATATGGAGGAACACCTATTAACCAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G42520.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G42520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g38670.1 (Oryza sativa), 3'ss of exon 1
------------------gttggggttctcttctgatgtcaagat----tcttcgctttggtagaagttagttagtttctcata----tcttgttctaatgat---ttttggcagATACATGATGAGGCTAAAAAGTTCTCTTACCAAACTGGTGTGAAGGTGGTTGTTGCATATGGAGGAACACCTATTAACCAGCAG
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gtgatggatgcgaagaaagtctttgttgctttgtcggtgcaggatatcatctctgatttgattttctttgacatgcatttgatgggcgctttgttatatttgtatgctcttgcagATTCATGAGGAGGCGAGAAAATTTTCCTATCAGACCGGTGTCAGGGTGGTTGTTGCATATGGAGGAGCACCTATTAATCAGCAG
upper sequence: AT2G42520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G26630.2 (Glycine max), 3'ss of exon 1
-----gttggggttctc--ttctgatgtcaagattcttcgctttggtagaagttagttagtttct--catatcttgttctaatgatttttggcagATACATGATGAGGCTAAAAAGTTCTCTTACCAAACTGGTGTGAAGGTGGTTGTTGCATATGGAGGAACACCTATTAACCAGCAG
|| | || | | ||| | | | |||| | ||||| ||| | | | | | | | | || | | | |||||||||||||||||| |||||||| ||||| ||||||||||| || ||||| ||||| ||||||||| |||| || | ||| |||
gtgcaattctgattttagatcctggtttgcattgccttcatatgtgtagatgttgatctatatatactaaaaactaaaatgttgttgtctcgcagATACATGATGAGGCCAAAAAGTTTTCTTATCAAACTGGTGTCAAAGTGGTGGTTGCTTATGGAGGAGCACCAATCACCCAACAG
upper sequence: AT2G42520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G15940.1 (Glycine max), 3'ss of exon 2
-----gttggggttctc--ttctgatgtcaagattcttcgctttggtagaagttagttagt---ttctcatatcttgttctaatgatttttggcagATACATGATGAGGCTAAAAAGTTCTCTTACCAAACTGGTGTGAAGGTGGTTGTTGCATATGGAGGAACACCTATTAACCAGCAG
|| | || | | ||| | | | |||| | |||| || | | | |||| | | | || | | | |||||||||||||||||| |||||||| ||||| ||||||||||| || || || ||||| ||||||||| |||| || ||||| |||
gtgcaattctgattttagatcctggtttgcattgccttcatatgtttagatgtctatctatatatactcaaaaactaaaatgttgttgtctcgcagATACATGATGAGGCCAAAAAGTTTTCTTATCAAACTGGTGTCAAAGTTGTGGTTGCTTATGGAGGAGCACCAATCAACCAACAG
upper sequence: AT2G42520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g07070.t01 (Vitis vinifera), 3'ss of exon 2
-------gttggggttctcttctg-atgtcaagattcttcgctttggtag------aagttagttagtttctcatatcttgttctaatgatttttg----gcagATACATGATGAGGCTAAAAAGTTCTCTTACCAAACTGGTGTGAAGGTGGTTGTTGCATATGGAGGAACACCTATTAACCAGCAG
|||| | | || ||| | | |||| | || | | | || | | | ||| || || || | ||||||||||||||| |||| |||||| || || ||||||||||| |||||||| ||||| || |||||| |||| || ||||| |||
gtgggattttggtttataccattgcatgctatgcatcttaggttgcgcaattttctatgtggaccatgtctacttatgttaccgccattgcattcgacttgcagATACATGATGAAGCTAGAAAGTTTTCCTATCAAACTGGTGTTAAGGTGGTAGTTGCTTACGGAGGAGCACCAATCAACCAACAGMapped 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|47829486|gb|CK119170.1|CK119170EST: TCTACCCTCTTGCAGTTATTCTCTCACCAACAAGAGAGTTGGCAAGTCAG ATACATGATGAGGCTAAAAAGTTCTCTTACCAAACTGGTGTGAAGGGTGGT
genomic: TCTACCCTCTTGCAGTTATTCTCTCACCAACAAGAGAGTTGGCAAGTCAGgttggggttc ... tttttggcagATACATGATGAGGCTAAAAAGTTCTCTTACCAAACTGGTGTGAAGG-TGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgctttggtagaagttagttagtttctcatatcttgttctaatgatttttggcagATACATGATGAGGCTAAAAAGTTCTCTTACCAAACTGGTGTGAAGGTGGTTGTTGCATATGGAGGAACACCTATTAACCAGCAG
ttctaat putative branch site (score: 2)
ttttt putative PPT
ttctaatgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggggttctcttctgatgtcaagattcttcgctttggtagaagttagttagtttctcatatcttgttctaatgatttttggcagATACATGATGAGGCTAAAAAGTTCTCTTACCAAACTGGTGTGAAGGTGGTTGTTGCATATGGAGGAACACCTATTAACCAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA