Sequence
atgc intronic sequence ATGC exonic sequence...catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttctgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G74030.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 2
catatttctcttttggttccaaa-gttcttctattctttggattatcacaaagaattgtttttctgatagtaatgcatttaatgtactttgttgat--tacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
| | ||| || | | | | | | | || || || || || | | | | | ||| || ||||||||| ||| | | ||||| || || || | || |||||||||||||| || ||||| ||||||||||| || ||||| || ||||||||||| |||||
---acattggcaacagttacatctgcgcatttgacttgtagtttgctctcgtcttttaattctcaaatgtttgtcttctgagatttacctgtccatgttacagTTTACCATGCCCTAAAGGGCATCATTAAGGCGAAATATGGTCAAGATGCATGCAATGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 2
catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttt-tctgatagtaatgcatttaatgtactt-tgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
||| | | | | | || || | || | | | || ||| || | | ||| | ||| | || | |||||||| ||| ||||| | || || || | || |||||||||||||| || |||||||||||||||||||| ||||| || ||||||||||| |||||
--tatgttgtatcagtgaatagctatattgggactatttgcttctgctagctggtcacttcatcttctaacctcacttggaatatccttgttctggtaacagTTTACCATGTCCTGAAGAGCATCATTAAGTCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 2
catatttctcttttggttccaaagttcttctatt----ctttggattatcacaaagaattgtttt-tctgatagtaatgcatttaatgtactttgt-tgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
| | || | ||| ||| || ||| | || | | | || ||| || | | ||| | ||| | || | |||||||| ||| ||||||| || || || | || |||||||||||||| || |||||||||||||||||||| ||||| || ||||||||||| |||||
------tttgttataaaagtaaacatctatatttgggatttttgcttcttctagctggtcacttcatcttctatcctcacttggaatatccttgttatggtaacagTTTACCATGTCCTGAAGGGCATCATTAAGGCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 3
catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttc-tgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
| | | | | | || ||| ||| ||| || || || | | | ||| | | | | | || || | |||||||||||| ||| ||||| |||||||| | || ||||| |||||||| |||||||| |||||||||||||| ||||| || |||||||||||||||||
-ctgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctacatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 2
catatttctcttttggttccaaagttcttctattctttggat-tatcacaaagaattgtttttctgatagtaatgcatttaatgtactt--tgttgatt--acagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
| | | | | | || ||| ||| ||| || || ||| | || | | | || | ||| || |||| | || | || | |||||||||||| ||| ||||| |||||||| | || ||||| |||||||| |||||||| |||||||||||||| ||||| || |||||||||||||||||
-gcacattatgtatagcac--aaattccataattttttcaatctaacaccagtgatc-tatatatggtgacaat-cagttaacttggttatttctggtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 1
catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttctgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGA-AGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG-----------------------------
| | ||| | || | | | || || || || || || || | | | | || | | || | || | || | | |||||||| | || ||||| |||||||| |||||||| |||||||||||||| ||||| || | |||||||||||||||
-----------gtagcagagaaaaatattagagtttccttcttctctttct---ttcttcttgggagggtcctagacctcgaatgctaggaaacattgagctgattttcagttcataacaaataatcaagGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCA
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 3
---------------------------------------------catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttc-tgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG----
| | | | | | || ||| ||| ||| || || || | | | | ||| | | | | | || || | |||||||||||| ||| | ||| | ||| | || ||||| |||||||| |||||||| |||||||| ||||| ||||| || |||||||||||||||||
gtattacatatgatttgatagctaatcttaattccatttttcctgactgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctatatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAGGGGTA----CAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttctgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
| | | |||| |||| | |||| || || | | || | | || || | | | | | || || |||||||||||||| ||||||| || ||||| | || ||||| |||||||| || ||||| || ||||| || || ||||| || |||||||| ||||| ||
ttctatgattatgcagttctttagttgtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAGMapped 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|47832245|gb|CK121929.1|CK121929EST: ACCTGTAGGAGCTACCTCATTCTCGGAGGNCTTCCAGATGGGAAGTGAAG TTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTT
genomic: ACCTGTAGGAGCTACCTCATTCTCGGAGGCCTTCCAGATGGGAAGTGAAGgtcagttagt ... ttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTT
EST:
gi|47831124|gb|CK120808.1|CK120808EST: ACCTGTAGGAGCTACCTCATTCTCGGAGGCCTTCCAGATGGGAAGTGAAG TTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTT
genomic: ACCTGTAGGAGCTACCTCATTCTCGGAGGCCTTCCAGATGGGAAGTGAAGgtcagttagt ... ttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacaaagaattgtttttctgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
ctttgtt CT-rich tract
atttaatgtacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttctgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - ttccaaa
- - - - - - - - - - - - - - - - - - - - - - tcacaaa