Sequence
atgc intronic sequence ATGC exonic sequencegtttgttgattgcctttcttttgctctttgacatagagttctactaactttggagatgtgagaaattgtaaagcgatacttattgactgtacatgatgaaactagaatcaagtaatttcctagttcctctgaatcttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55610.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g38150.2 (Oryza sativa), 3'ss of exon 4
----gtttgttgattgcctttcttttgctctttgacatagagttctact--aactttggagatgtgagaaattgtaaagcgatacttattgactgtacatgatg-aaactagaatcaagtaatttcctagttcctctgaatcttttagtctactaacttacagcttcactgtacttcaa--cgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
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gtatgtaagtgtgtttcataccatacatctcctggaaaagtatgaaacttcagtttttgcgtggtgctgctctttagc-tgctacttattg-ttatactgcttgtatgcctagccctagggccttgtcagtgtatatgcaaat----agccatgactttctaaccacactcacctataattcttttacagGATTCATCTGGTATATTCTGGGATAATGACAGTTTAGCAGGACTGTTGGCACTGGAACTGAAAGCTGATCTCCTTATTCTGCTCAGTGATGTGGATGGGT
upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 5
gtttgttgattgcctttcttttgctct--ttgacatagagttctactaactttggagatgtgagaaattgtaaa-gcgatact-tattgactgtacatgatgaaactag--aatcaagtaatttcctagttcctctgaatc-ttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
| | | || | | | |||||| | || | || || | || | |||| | |||| | | | | || ||| || ||| | | | | | || | || | |||| | | ||| | | || | | || | |||||||| | ||||||||||||||||||||||| ||||||| |||| || | |||| || ||||| |||||| | |||| || ||||| || || ||||
-----------gtttgtgttgtaccatgcatgacattaaatttcaacaatatttgc--tgcactgcttgataaatgtgatatcgtgctacttatgcaccttgaccttaaccaatgcatgagtctgttgattttttaaaagcattttcgatgtcatactcataaa--cagtttgtttt------tgcagGATTCATCGGGTATATTTTGGGATAATGACAGTTTAGCCGGTCTTTTGGCTATAGAACTTAAAGCAGATCTTCTTGTTCTACTCAGTGACGTGGATGGCC
upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G375504_T01 (Zea mays), 3'ss of exon 4
gtttgttgattgcctttcttttgctctttgacatagagttctactaactttggagatgtgagaaattgtaaagcgatacttat-tgactgtacatgatgaaactagaatcaagtaatttcctagttcctctgaatcttttagtc-tactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
|||| | | ||| | | | ||| | |||||| || |||||| || |||||| | | | | || || | | | || ||| | | ||| || | || || |||| | | | ||| ||||||| |||||||||| |||||||||||||| ||||| | |||| || | | || || ||||| ||||| | |||| ||||||||||| || || |
------------------gtttgtgttgtaccatgca----tgccttcttgataaatgtga-------tatcatgatactcatgcacctgtacctta----gcca--atgcaggagtctgttaaagtctcaatagcattttgtgatgctcaccaacagttcctttttac------------agGATTCATCTGGTATATTCTGGGATAATGACAGTTTAGCTGGTCTTTTGGCTATTGAACTTAAAGCAGATCTCCTTGTTCTACTAAGTGATGTAGATGGTC
upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 5
gtttgttgattgcctttcttttgctctttgacatagagttctactaactttggagatgtgagaaattgtaaagcgatacttattgactgtacatgatgaaactagaatcaagtaatttcctagttcctctgaatcttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
|| | || | || | | || | | ||||| | | | |||| | ||| | | | | | || ||||| || | | | || | || | | |||||||||| |||||||||| |||||||||||||| |||| ||||| || | ||| || || ||||||||| | || | || |||||||| || || |
---------------------------------------------------------gtctgtt-ttcttaattgcttctgcacggccgtacacca--accttccaatctaataacagctgggcccttggttgtgttcctacttacta-ctgattgtaataatgaatttaa---tttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC
upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G41850.1 (Glycine max), 3'ss of exon 2
gtttgttgattgcctttcttttgctctttgacatagagttctactaactttggagatgtgagaaattgtaaagcgatacttattgactgtacatgatgaaactagaatcaagtaatttcctagttcctctgaatcttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
|| | | | || | ||| | |||| | | | | || ||| | | || || | || ||| | || | | ||||||||| |||||||||||||||||||||| || ||| | ||||| || | | ||| | ||||| |||||| | || | | |||||||| || || |
-------------------------------------------------------------------------------ttttcttttccagattgaaagtttagtttgaagttgctgcat--tctttccagttctatatatttaagtacatcaagtgtcattaacgttttttttgtgcagGATTCTTCTGGTATATTTTGGGATAATGATAGTTTATCTGCTCTGTTGGCCTTGGAGTTAAAAGCCGATCTTCTTGTTTTGTTGAGTGATGTAGAAGGTC
upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 2
gtttgttgattgcctttcttttgctctttgacatagagttctactaactttggagatgtgagaaattgtaaagcgatacttattgactgtacatgatgaaactagaatc--aagtaatttcctagtt-cctctgaatcttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
|| ||| | || || | | | | || || | | || || ||| | | | || | || ||| | | | | ||||||||| |||||||||||||||||||||| || ||| | ||||| || | | ||| | ||||| |||||| | || | | |||||||| || || |
------------------------------------------------------------------------------------gaatgtttagtttggaattgctacctggaatacttgctttattgtttccatttctatctattcaagtacatcaagtgtcattaacgtattttatgtgcagGATTCTTCTGGTATATTTTGGGATAATGATAGTTTATCTGCTCTGTTGGCCTTGGAGTTAAAAGCCGATCTTCTTGTTTTGTTGAGTGATGTAGAAGGTC
upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 5
gtttgttgattgcctttcttttgctctttgacatag-agttctactaactttggagatgtgagaaattgtaaagcgatacttattgactgtacatgatgaaactagaatcaagtaatttcctagttcctctgaatcttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
||||||| ||| || | | | | || || || || || ||| || ||| || | | |||| || | || | | ||| | || || || | | || || | | | ||||| || ||||| | ||| ||| ||||||||| |||| |||||||||||||||||||| ||| | ||| | || | | || | |||||||||||| | ||| | | |||||||| ||||| |
gtttgtt-attctacttgtctggtttgttatcagagcagaact--taatcttagagctgattg----cttcaagctatgcaccttta----------taaaaaaaaaaacaggtgacgtatgaga----ctagactagagaat------acttaaagtgtcactaaa--tcattttatgcagGATTCTTCTGGCATATTTTGGGATAATGACAGTTTATCAGCTTTATTGGCATTGGAATTAAAAGCTGATCTTCTTATTTTGTTGAGTGATGTAGAGGGTC
upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 5
gtttgttgattgcctttcttttgctctttgacatagagttctactaactttggagatgtgagaaattgtaaagcgatacttattgactgtacatgatgaaactagaatcaagtaatttcctagttcctctgaatcttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
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------------------------------------------------------------------------aaggtccttttaaatcctgtcctatgctcttagtttcattgaatcctgaaatttattta----tcttgatccaccc-----ctgtctgattatattaactcttttgcagGATTCTTCGGGAATATTTTGGGATAATGACAGTTTAGCAGGCCTACTGGCTTTGCAGCTAAAGGCTGACCTCCTTGTTCTATTGAGCGATGTAGATGGTCMapped 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|164077706|gb|ES056476.1|ES056476EST: AGTTTTCAATGAGAATGATGCTATAAGCACTCGCAGAGCCCCCCTACAAG GATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCT
genomic: AGTTTTCAATGAGAATGATGCTATAAGCACTCGCAGAG-CCCCCTACAAGgtttgttgat ... acgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCT
EST:
gi|164018284|gb|ES120001.1|ES120001EST: CAGTTTTCAATGAGAATGATGCTATAAGCACTCGCAGAGCCCCCTACAAG GATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTC
genomic: CAGTTTTCAATGAGAATGATGCTATAAGCACTCGCAGAGCCCCCTACAAGgtttgttgat ... acgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctgaatcttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
aatctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttgattgcctttcttttgctctttgacatagagttctactaactttggagatgtgagaaattgtaaagcgatacttattgactgtacatgatgaaactagaatcaagtaatttcctagttcctctgaatcttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
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