Sequence
atgc intronic sequence ATGC exonic sequencegtaataacaactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G02560.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 5
gtaataacaactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
||| | || | | || | | | | || | | || || |||| ||| ||||| | || ||| ||||||||||| ||||| |||| ||| ||| |||||||||| |||||||||||| |||| |||||||| ||
---gtaatagctcatctaacatagtatgtctgcgttagctgcttcaat---taat-actaatgcattttcgttttctgttagGAATGGCTATATTTGATACAATGAAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G01550.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------gtaataa-caactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
| ||| || || | ||| | | ||| | | | | ||| | | | || ||| || | | ||| ||||||||||| ||||| |||||||| ||||| ||||||||||| |||||||||||||| |||| |||||
gtaatagttttttagttaaaactatcttgctttgttttttttattattatattatattcatctacatgggctaaaaatatattgtatcccaaatattaaaatgctttctttgttattcttttcccct---tagGAATGGCTATATTTGATACAATGAGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCAGCTAG
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G01510.2 (Glycine max), 3'ss of exon 5
------------------------------------------------gtaataa-caactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
| ||| || || | ||| | | ||| | | || | ||| | | | || ||| || | | ||| ||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||||||||| |||| |||||
gtaataattttttagttaaaactatcttgcattgtcttttattattatattatattcatctacatgggctgaaaatatattgtatctcaaatattaaaatgctttctttgttattcttttcccct---tagGAATGGCAATATTTGATACAATGAGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCGGCTAG
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G37880.1 (Glycine max), 3'ss of exon 4
------------------------------------------gtaataacaactttgtc--agcttac---tctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
||| | | | || || | |||| | | || || ||| | ||||| | | || | | || ||||||||| ||||| ||||| |||||||| || || |||||||||||||||||||| |||| || || |||||
gtaataattattttatgtgaatctgccctgcattagtttactgtattca-atctatgcctagacttaaaaatgcaatgcgttattttattttaaaaactaatg--tgcttcacttttcctttctgttagGCATGGCAATATTTGATACAATGAGGCATATTCGACCTGATGTGTCCACTGTTTGCATTGGACTGGCAGCTAG
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G40480.1 (Glycine max), 3'ss of exon 4
------------------------------------------gtaataacaactttgtc--agcttactcttt--atcttttttccggttttatggttaatgactcg-tgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
||| | | | || || | |||| | || || | ||||| | |||| | | || | | ||| ||| |||||| ||||| ||||| |||||||| || || |||||||||||||||
gtaataattattttttgtgaatctgccctgcattagtttactgtattca-atctatgcctagacttaaaaatgcaatgcattattttattttaaaat--atgatgtgcttcacttttcctttttgtcagCCATGGCAATATTTGATACGATGAGGCATATTCGACCTGATGTGTCCACT-----------------------
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------gtaataacaactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
| || | || | | || | | | || | | |||| | || ||| | | | | ||| | | ||||||||||||||||||| || |||||||| ||||| |||||||| |||||||| |||||||| ||||| || ||
gtaatttctgtcttacaataaatttttcttcacactggtactagtttatttaactgagcatggagacttgtacaggttcttattttcttgaattcttccttattta-tcccctcagGCATGGCTATATTCGACACAATGAGGCATATCCGACCTGATGTTTCCACTGTGTGTGTTGGACTAGCAGCCAGMapped 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|125289367|gb|EL303452.1|EL303452EST: GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG GCATGGCTATATTCGATACTATGAGGCACAT
genomic: GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaa ... ctttacccagGCATGGCTATATTCGATACTATGAGGCACAT
EST:
gi|125166336|gb|EL192182.1|EL192182EST: GGTGGATCAGTTACAGCTG GCATGGC-ATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTG
genomic: GGTGGATCAGTTACAGCTGgtaataacaa ... ctttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTG
EST:
gi|124709267|gb|EH800669.1|EH800669EST: CTGGTGGATCAGTTACAGCTG GCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTG
genomic: CTGGTGGATCAGTTACAGCTGgtaataacaa ... ctttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
ctcttac putative branch site (score: 3)
tctcttactttaccc CT-rich tract
ttacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataacaactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT