Sequence
atgc intronic sequence ATGC exonic sequencegtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.4 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
--gtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
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gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattat-acagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
--gtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG------
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gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattat-acagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 21
---gtatttcattactg--ttcacttggccgt--ttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
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gtaggcttctgcaattgaatgcatcttgccctactcagtaacatcttgtatcggacattg--tatgttgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G443953_T02 (Zea mays), 3'ss of exon 20
-------------gtatttcattactg--ttcacttggccgt--ttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
| || | || | || | ||| | | | || ||| ||| | | || ||| || | | | || || ||||||| || || |||||||| || ||||||||||| ||||| ||||||||||||||||| || || || | |||||| | || ||| |||
tggttgataggtaggcttctgcaattgaatgcatcttgccctactcagtaacatcttgtatcggacattg--tatgttgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
-------------------------------------------------------------------gtatttcatt--actgttcacttggccgt---ttggaaaaatcaaatatgtgtcttttgttatctttatgacaa---gaaattatct-tgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
||||||||| || | | ||| || || | | || | || || | | | || | | || || ||| | |||||| |||||||| ||||||||| | |||||||| ||||| ||||||||||| ||| | |||||| | | | ||||| | || |||| ||||
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 20
----gtatt-tcattactgttcacttggccgtttggaaaaat-caaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
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gtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatat-tccacttttgggatgatactgaagcattctctttgcagCAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAAGGTCTCAGAGATAGTCGCTCTGTGGAGGAAAGACCTTAATAAGMapped 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|125289748|gb|EL303833.1|EL303833EST: TTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAG TAACCGGATACCAGAAGCTGCT
genomic: TTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgtatttcatt ... atcttgacagTAACCGGATACCAGAAGCTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
ttatctt CT-rich tract
ttttgttatctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG