Sequence
atgc intronic sequence ATGC exonic sequencegttaacttaagtgcttactttcaggggttttacgcgccagtgtttgctttcatctcagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G58560.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
------------------------gttaacttaagtgcttactttcaggggttttacgcgccagtgtttgctttcatct--cagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT
| || || ||| || | | | | | || |||| ||| | || | || ||| | | | | | |||||| | ||||||||||| | | |||||||| || || |||||||| ||||||||||| ||| || || ||||||||||| ||||| || |||||||| || ||||||||
gttggtgcatggagactcacccacgcacacagtagactttaattctatgtttgcagcttctgtatattcattttcctctaataagattgtgcttattcttttgatgatggcgatgtttgttctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
gttaacttaagtgcttactttcaggggttttacgcgccagtgtttgctttcatctcagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT
| || |||| | |||| | | | || || || | | ||| ||| | || ||| | || |||||| | |||||||||| | | |||||||| || || |||||||| |||||||| || || || || |||||||||||||||||||| | |||||| || ||||||||
tctgtgtttgcagcttctgtatctccatttttctggaataagattaaaggca-ctaattgtgcttattcttttgataatgaccatg---tttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
gttaacttaagtgcttactttcaggggttttacgcgcc-agtgtttgctttcatctcagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT
| || || | ||| | | | | | || |||| | | | |||| || || || || || || ||||||||||| | | ||||| || || ||||| | ||||||| ||| ||||||||||||||||| ||||| || || |||||||| || ||||||||
------gtgagcatggtgttatatcattttgataaacttaatatctgt----atcttgg-tcacatttttatg----aaaagatatgacttgtg----gtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 10
gttaacttaagtgcttactttcaggggttttacgcgc-cagtgtttgctttcatctcagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT
| || || | ||| | | | | | || | ||| | || | | ||| || || || || ||||||||||| | | ||||| || || ||||| || ||||||| ||| ||||||||||||||||| ||||| || || |||||||| || ||||||||
------gtgagcatggtgttatatcattttgataaacataatatctgtatcttgttcacaattttatg---------aagagatatgacttgtg----gtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTGCTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------------gttaacttaagtgcttactttcaggggttttacgcgccagtgtttgctttcatctcagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT
|| | || | ||| || || || | | | || || | | | ||| ||| || ||| ||| | ||| || ||| |||| ||| | |||| |||||||| ||||||||||| |||||||| || |||||| || |||||||| ||||| ||||| || ||||| |||||||| ||
gtaatctttttcctacatgtcggtttgcatctttttcctatat-tttatttacacatgtgcttcatacttgtagtttgtgccgttattgatg--tttaggattctctaataaataagatttgtg----gttccagCCGACTCTTTAACGGTGGAATCATTGTTGGAACTCTTGGATGAGGATAGCTTGAGAAAAGACACAGCACTTCCTTCTCCGGAGTGGTCCTCTGATCATATMapped 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|116428969|gb|EG471561.1|EG471561EST: CAACTGTACCAGGGACTTTATAGGCACACTTGATTACATATTTTACACAG CGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCT
genomic: CAACTGTACCAGGGACTTTATAGGCACACTTGATTACATATTTTACACAGgttaacttaa ... tttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCT
EST:
gi|86059624|gb|DR355381.1|DR355381EST: CAACTGTACCAGGGACTTTATAGGCACACTTGATTACATATTTTACACAG CGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCT
genomic: CAACTGTACCAGGGACTTTATAGGCACACTTGATTACATATTTTACACAGgttaacttaa ... tttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatctcagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT
ctttttgttttgtttc CT-rich tract
tttttgttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaacttaagtgcttactttcaggggttttacgcgccagtgtttgctttcatctcagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC