Sequence
atgc intronic sequence ATGC exonic sequencegttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattacttaacaattggtttcttctgatctcagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08530.1 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
gttagaagctgactg-atgactttgtttttttctataaaaacaactgagctacattactt--aacaattggtttcttctgatctcagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
||| | || | | | | | || | || ||||| | || | | || | || ||| || || || | ||||||||||| |||| |||| | || ||||||||| ||||||||||||||||||||||||||||||| ||||| ||| |||||||| | || || ||||| |
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gttagaagctgactg-atgactttgtttttttctataaaaacaactgagctacattactt--aacaattggtttcttctgatctcagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
||| | || | | | | | || | || ||||| | || | | || | || ||| ||| || |||| ||||||||||| |||| |||| | || ||||||||| ||||||||||||||||||||||||||||||| ||||| || |||||||| | || || ||||| |
gtttgtttcttatggcagggccttctattggtctatcagttttgctccgtttcaaaattttgaactatttcattattctttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 2
gttagaagctgactgatgactttgttttt---------ttctataaaaacaa-----ctgagctacattacttaacaattggtttcttctgatct--------cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
||||| | |||| ||| | || || | || ||| || | | | | | | || | || || | || | ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| ||||||||||||||||| ||||| || |||| || | || || ||||| |
gttagcatctgaatgaaaatttatttccttagcgcactttggatagaagccctgttttcaaattccttcccccaaaatctgacttgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCTGTGAATGAAGCCTTGAACGAACTTTATGTTGAAGAGG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
gttagaagctgactgatgactttgttttttt-----ctataaaaacaa---ctgagctacattacttaacaa---ttggtttctt-ctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
||||| | |||| || | || || || || | || | || ||| | ||| ||| || || | |||| || ||| ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| || |||||||||||||| ||||| || |||||||| | || || ||||| |
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
gttagaagctgac-----tgatgactttgtttttttctataaa-aacaactgagctacattact----taacaat-tggtttcttctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
| ||| |||| || | |||||| || | || | | | | | || | | || ||| || || | || ||| ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| |||||||||||||| || ||||| || ||||||| | || || ||||| |
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattacttaacaattggtttcttctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
| | ||| || || | | | | | | | || | || || | || ||| ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| |||||||||||||| || ||||| || ||||||| | || || ||||| |
-----------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 9
gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattacttaacaattggtttcttctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
| | ||| || || | | | | | | | || | || || | || ||| ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| |||||||||||||| | ||||| || ||||||| | || || ||||| |
-----------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCATGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
gttagaagctgactgatgactttgtttt---------tttctataaaaac---aactgagctacattacttaacaattggtttcttctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
||||| | |||| ||| | | | | ||| ||| || | | | | | | | || | || || | || ||| ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| |||||||| ||||| || ||||| || |||||||| | || || ||||| |
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtc-ccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
gttagaagctgactgatgactttgtttt---------tttctataaaaacaactgagctacattacttaacaat-tggtttcttctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG-----------------------------------------------------------------------
|| || | |||| ||| | | || | ||| ||| || | | | | || ||| || || | || ||| ||||||||||| |||| |||| | || ||||| ||| ||||| ||||||| |||||||||||||| | |||| || |||||||| | || || ||| |
gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgattcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
---gttagaagctgactgatgactttgtttt--tttctataaaaacaactgagctacatt--acttaacaattggtttcttc-tgatct----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
| || | | || | || ||| || | | ||| | |||| ||| | | | |||| |||| | |||||||||| | |||||| |||||||||||||| ||||||||||||| |||||||| |||||||||||||| || || ||||| ||||| || || || |
gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
---gttagaagctgactgatgactttgtttt--tttctataaaaacaactgagctacatt--acttaacaattggtttcttctgatct----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
| || | | || |||| ||| || | | ||| | |||| ||| | ||| || | | |||| | |||||||||| | |||||| ||||||| |||||| ||||||||||||| ||||| || |||||||||||||| || |||||||| ||||| || || || |
gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattac-ttaacaattggtttcttctgatct----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
|| || | | || | ||| || ||| | || ||| || ||| |||| | |||| | ||||||||||| | |||||| | || || || |||||||||||||| ||||||||||| |||||||||||||| || ||||||||||||| || || || |
gtaggatgaatattggcaaaa--atttcattagatatcagttgttgcatgccataacactaatgggaaatttcat-tgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 25
gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattact-taacaattggtttc-ttctgatct----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
|| || | | || | | ||| || ||| | || ||| ||| ||| ||| | | || | ||||||||||| | |||||| | || ||||| ||| |||||||||| |||||||| || |||||||||||||| || ||||||||||||| || || || |
gtaggatcattagtggtaaaa--atttaattagatattagttgttgcatgccataactctaatgggaaacttcactttaatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCATATATGGTTGCAGTTCAAAGCAACAACGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTTGAGGAGG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
----------------------------------------gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattacttaacaattggtttcttctgatctcagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
| |||| | | || || | | || | || || || ||| || ||| | ||| ||||| |||||| | | |||| | |||||||| ||| ||||||||||||| |||||||| |||||||| ||||||||| |||||| ||| || || || || |
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgtt--ttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGGMapped 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|116468291|gb|EG510883.1|EG510883EST: TACTTGCG-TGCGGTTAGACCATACTCGTGTTGTTGATATAATGCGGAAG GCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAAC
genomic: TACTTGCGTTGCGGTTAGACCATACTCGTGTTGTTGATATAATGCGGAAGgttagaagct ... ctgatctcagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAAC
EST:
gi|164096881|gb|ES059314.1|ES059314EST: TACTTGCGTTGCGGTTAGACCATACTCGTGTTGTTGATATAATGCGGAAG GCTGGTCACTTGCGTCTTA
genomic: TACTTGCGTTGCGGTTAGACCATACTCGTGTTGTTGATATAATGCGGAAGgttagaagct ... ctgatctcagGCTGGTCACTTGCGTCTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctataaaaacaactgagctacattacttaacaattggtttcttctgatctcagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
ttctgat putative branch site (score: 3)
tttcttctgatctc CT-rich tract
attacttaacaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattacttaacaattggtttcttctgatctcagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG