Sequence
atgc intronic sequence ATGC exonic sequencegtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttatctctgtttcacagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G25760.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 13
------gtattcttgttttactccttttgaatgcaggtgtaacagttatt-tccgttttatctctgt--------ttcacagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
|||| | | || | || ||||| ||| | | || || | || | | | | | | | | ||||| || | ||| ||| |||||||||||||| |||||||| ||||||||||| |||||||| |||||||||| ||| ||||| ||||| || | ||||
gagaagccattcacagcgcaaacactt-gggtgtct-tgtaatgtttactgttggtatttattatgagcaagaagccaagaactgacttgaatgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 12
gtattc--ttgttttactccttttgaatgcaggtgtaacagttatttccgttttatctctgtttcacagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
||| | || | | ||| | ||| | |||| | || | ||| || || | ||| | || ||| || |||| |||||||||||||||||| |||||| |||| || ||||| |||||||| || || |||||||| || |||||||| || || |||||
gtaaccagttaaagcatgctgtttcagtgctattcctgtc-ttataatgtataaattattctttgactaactt-agcatgcttttttagGAACAATGTATACACAACAATCCTACAAAGTAAGTGATACTTTCCCTTTCAAATGGATAAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
----------gtattcttgttttactccttttgaatg--caggtgtaacagttatttccgttttatctctgtttcacag-ttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
|| | | || | | | | | | || | ||| || || | | | || || | | || | ||||||| || ||| ||||||||||||||||| || || || |||||||||||||||||||| || ||||||| ||| || || ||||| || | |||||
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
gtattcttgttttactccttttgaa-tgcaggtg-taacagttatttccgttttatctctgtttcacagtt-------------ttcatcatttgtattc-agGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
|| | ||| || | | || || ||| |||| || | | || | || | | | | | | | ||| || ||| || || ||| || || ||||||||||| || ||| | ||||||||||| |||||||| |||||||||| ||| || || ||||| || | |||||
---ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
---gtattcttgttttactccttttgaatgc-aggtgtaacagttatttccgttttatctctgtttc--------acagttttcatcatttgtattc-agGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
|| | | ||| |||| | || | | ||||| || | || | | | | | | ||| || ||| || || ||| || || ||||||||||| |||||| | ||||| ||||| |||||||| |||||||||| ||| || || ||||| || | |||||
ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
---gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttatct---------ctgtttcacagttttcatcat-ttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
| || | | ||| | | | ||| |||||| | || | | |||| | | || | | | | | |||| || || ||| || ||||| |||||||| || || || || || |||||||||||||| ||||| |||| ||| || ||||||||||| | |||||
gtcaagctgcgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
----------------------gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgtt--ttatctctgtttcacagttttcatc--atttgtatt--------cagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
| ||| ||| || ||| | || | | | ||||| | |||| | | | | || | ||||| ||| ||| |||||||| ||||| |||||||| |||||||||||||| ||||| || |||||||| || ||||| ||||| ||||| |||||||| || | |||||
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 13
-------------gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttat------ctctgtttcacagttttcatcatttgtattc--------------agGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
|| || || | | | ||| || || || || | || | ||| || | | ||||| | | | | | ||||||| ||| |||||||| ||||| |||||||| |||||||||||||| ||||| || || ||||| || ||||||||||| ||||| |||||||| || | |||||
gttaatacccctgaagtttttattcttcatgtattgtatttggg-gtggcaataatatacgtattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------------------------gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttatctctgtttcacagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
| || | || | |||||| || | | ||||| | | ||| | ||| || | | || ||| |||||||| || || |||||||| |||||||||||||| ||||| || |||||||| || ||||| ||||| ||||| |||||||| || | |||||
gttaatcccctgaagtatttattcttcatgtattgtgtctttgggatggcgataattggcttgagtttagatgatcacatgtt-ttgcttttgcatatt--ttgactggttatgtttaaactgtcttcttacttgtatttggattgatcct-tttagGTACCCAGTACTTGCAGCAATCCTATAAAGTCAGTGATTCATTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 13
-----------gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttatctctgtttca--cagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
|||| | |||| | || | |||| ||| | | ||| ||| | | | || || || || ||| || || |||||||| || ||||| ||||||||||| || ||||| || ||||||||||||||||| ||||| || || || |||||||| | |||||
gtcagtgtgacttatttaaaaccaatcattttttgagacaatgacttcttttatgattgttatctgtctcttttaacctctgttaatttactgaatatagGCACGCAATATTTACAGCAGTCCTATAAAGTCAGTGAGTCATTTCCATTTAAGTGGATAAATAAAAAATGGAGAGAGGGTTTCTATGTTACTGCTATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 13
gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttatctctgtttcaca-gttttcatcat-ttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
|| | || |||| || | || | | ||||||| | ||| | | ||||| ||| | |||| || || || || ||||| || |||||||| |||||||| |||||||||||||||||||||||||| |||||||| || || ||||| || || |||||
-----gttagtctaacatatttg---gctgatggatttctatgacaaaatttatctatattttgcttgacttcatttcattgactccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCAAGTGGATAAATAAAAAATGGAGGGAGGGTTTCTATGTCACCTCTATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttatctctgtttcacagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
| | ||| | |||||| | | | | || | | | | || ||||||| | || |||||||| |||||||| || ||||| ||||| ||||||||||| || ||||||||||||||||||||||| || || || |||||
--------------------------gtat-tgtcgctgttattgatggccactggcattgtcgctgacg-cgtgtttcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttatctctgtttcacagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
| | ||| | |||||| | | | | | | | | | ||| ||||||| | || |||||||| |||||||| || ||||| ||||| ||||||||||| || ||||||||||||||||||||||| || || || |||||
--------------------------gtat-tgtcgctgttattgatggccactggcattgttgctgacg-cgtgattcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGCMapped 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|116431236|gb|EG473828.1|EG473828EST: AGCAGTGGCAGGAGCAAATAGTGGGAACTCATTCGTGGTTATGTCAAAAG GGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCA
genomic: AGCAGTGGCAGGAGCAAATAGTGGGAACTCATTCGTGGTTATGTCAAAAGgtattcttgt ... ttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaacagttatttccgttttatctctgtttcacagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
gtgtaac putative branch site (score: 3)
atttgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttatctctgtttcacagttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG