Sequence
atgc intronic sequence ATGC exonic sequence...tccaaacatgaaagattgggtgtacttagactaatgaaaccactatacgagtactatctgtttcttgttttttgtgctgactggtttgtaatatcaccagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52570.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G30230.1 (Glycine max), 3'ss of exon 4
------------------------------tccaaaca-tgaaagattgggtgtacttagactaatgaaaccactatacgagtactatctgtttcttgttttttgtgctgactggtttgtaatatc--accagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
| || | | | | | | | | | |||| | | | ||| || | | | | || | | |||| | | ||||| || ||||| ||| ||||||| ||||| |||||||| || ||||||||| | || || |||||||||||||| ||||||||||||||||| || |||
gtgagtcagtgtatctttgataatctaatttttaattaatcccttaattaggatccattaattaattgtagtgatttgacggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G30230.2 (Glycine max), 3'ss of exon 4
--------------------------tccaaaca-tgaaagattgggtgtacttagactaatgaaaccactatacgagtactatctgtttcttgttttttgtgctgactggtttgtaatatc--accagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
| || | | | | | | | | | |||| | | | ||| || | | | | || | | |||| | | ||||| || ||||| ||| ||||||| ||||| |||||||| || ||||||||| | || || |||||||||||||| ||||||||||||||||| || |||
gtcagtgtatctttgataatctaatttttaattaatcccttaattaggatccattaattaattgtagtgatttgacggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G37560.2 (Glycine max), 3'ss of exon 4
-----tccaaacatgaaagattgggtg-tacttagactaatgaaaccactatacgagtactatctgtttcttgttttttgtgctgac--tggtttg-----taatatc--accagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
|| || | | | || | | || || | | | ||| ||| ||| || ||| ||||||| | || | | ||||| || ||||| ||| | ||||| ||||| |||||||| || ||||||||| | || || |||||||||||||| ||||||||||||||||| || |||
gtaagtcagtgtatctttcgtaatctaattttttaatccctcaattaacggtttcattgggatccgttaattgaaattaagaatgatagtggtttgactgttcatctttgagcagGGCCTTGGAATCACGGTATTTGGGATGGCCTACATGTTTGTCCACGATGGATTAGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 4
--tccaaaca----tgaaagattgggtg-tacttagactaatgaaaccactatacgagtactatctgtttcttgttttttgtgctgactggtttgtaatatcaccagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
||||| | | ||| | | | |||||||||| | | || | || | || | ||| | | || || || | ||| | ||||| || ||||| || | ||||| ||||| |||||||| || ||||||||| | || |||||||||||||| || || ||||| |||||||| || || |
ttaccaaatactaataaaataataattactacttagacttttaatgacattg-----atattgattgaacact-tttactaagatgccttcttca-actatgaacagGGTCTTGGAATTACTGTCTTTGGGATGGCCTACATGTTTGTACACGATGGATTGGTTCACAAGAGATTCCCGGTGGGCCCCATAGCCAACGTGCCCTATC
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G29790.1 (Glycine max), 3'ss of exon 4
---tccaaacatgaaagattgggtgtacttagact--aatgaaaccactatacgagtactatctgtttcttgttttttgtgctgactggtttgtaatatcaccagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
| | || | || || |||||||||| ||||| | | | || | || || || | | | | || | ||| | ||||| || ||||| ||| | ||||| ||||| |||||||| || ||||||||| | || || ||||||||||| || || |||||||| ||||| || || |
aaataccaataaaaataataattattacttagactttaatgacattgatct-tgattgaacacttttactaagata----gatagataccttcaactatgaacagGGTCTTGGAATTACGGTCTTTGGGATGGCCTACATGTTTGTACACGATGGATTGGTTCATAAGAGATTCCCGGTGGGCCCCATTGCAAACGTGCCCTATC
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------tccaaacatgaaagattgggtg--tacttag-actaatgaaaccactatacgagtactatctgtttct---------------tgttttttgtgctgactggtt---tgtaatatcac-cagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
| | || | || | ||| || | | ||| || | | | | | || | ||| ||| | | | || ||| || | ||| | || ||||| || ||||| || ||||||||||||| |||||||| || |||||||| || || |||| |||||| || || || |||||||| ||||| || ||
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgtttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATTMapped 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|86078127|gb|DR373884.1|DR373884EST: TGTCTGTGTTAGAGATGTTTGGTACATTTGCTCTTTCCGTTGGTGCTGCC GGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGA
genomic: TGTCTGTGTTAGAGATGTTTGGTACATTTGCTCTTTCCGTTGGTGCTGCCgtaagtttca ... atatcaccagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacgagtactatctgtttcttgttttttgtgctgactggtttgtaatatcaccagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
tgctgac putative branch site (score: 2)
tttgtaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccaaacatgaaagattgggtgtacttagactaatgaaaccactatacgagtactatctgtttcttgttttttgtgctgactggtttgtaatatcaccagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA