Sequence
atgc intronic sequence ATGC exonic sequencegtaactgcttatccatttgaactcttttaacttgcaccgcgctgtaagactaaatgaatcggttgaaaaagGCGGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGGATGCTGCTTGAGAGAGTGAGATTTACATTGGATGGCTTAGAATGTAATA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11720.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G42590.1 (Glycine max), 3'ss of exon 1
-----------gtaactgcttatccatt--tgaactcttttaacttgcaccgc----gctgtaagactaaatgaatcggttgaaaa---------agGCGGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGGATGCTGCTTGAGAGAGTGAGATTTACATTGGATGGCTTAGAATGTAATA---
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ttatggaagaaaacactgatgaactactgttacatacttttggcatgattcacaactgttacaagcttaaacaaaatatttacaatttttcttgtgatagGACAGCCCTCGGCAACCGCAGGATTTGGGGAGAAATATTCCTATGTGGATGCTGCTTGAGAGAGTGAGATTTACCTTAGATGGTATCGAATGTAACAAAA
upper sequence: AT4G11720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G09710.1 (Glycine max), 3'ss of exon 8
---------------gtaactgcttatccatttgaactct---tttaacttgcaccgcgctgtaagactaaatgaatcggttgaaa--------aagGC-GGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGGATGCTGCTTGAGAGAGTGAGATTTACATTGGATGGCTTAGAATGTAATA---
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ttatggaagaaaacagtgatgaactacttttacatactttcggcatgattcacaac-tgttataagcttaaacacaatatttacaatttttcttgtgacagGGCAGCCCTGGGCAACCACAGGATTTGGGGAGAAACATTTCTATGTGGATGCTGCTTGAGAGAGTGAGATTTACCTTAGATGGTATTGAATGTAACAAAA
upper sequence: AT4G11720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G02850.1 (Glycine max), 3'ss of exon 8
---------------gtaactgcttatccatttgaactcttttaacttgcaccgc----gctgtaagactaaatgaatcggttgaaa--------aagGC-GGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGGATGCTGCTTGAGAGAGTGAGATTTACATTGGATGGCTTAGAATGTAATA---
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ttatggaagaaaacagtgatgaactact--tttacatactttcgacatgattcacaactgttacaagcttaaacaaaatatttacaatttttcttgtgacagGGCAGCCCTGGGCAACCACAGGATTTGGGGAGAAACATTTCTATGTGGATGCTGCTTGAGAGAGTGAGATTTACCTTAGATGGTATTGAATGTAACAAAA
upper sequence: AT4G11720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G38410.1 (Glycine max), 3'ss of exon 4
---------------gtaactgcttatccatttgaactct---tttaacttgcaccgcgctgtaagactaaatgaatcggttgaaa--------aagGC-GGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGGATGCTGCTTGAGAGAGTGAGATTTACATTGGATGGCTTAGAATGTAATA---
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ttatggaagaaaacagagatgaactacttttacatactttcggcatgattcacaac-tgttacaagcttaaacaaaatatttacaatttttcttgtgacagGGCAGCCCTGCGCAACCACAGGATTTGGGGAGAAACATTTCTATGTGGATGTTGCTTGAGAGAGTGAGATTTACCTTAGATGGTATTGAATGTAACAAAA
upper sequence: AT4G11720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv02s0025g04090.t01 (Vitis vinifera), 3'ss of exon 7
------------------------gtaactgcttatccatttgaactcttt------taacttgcaccgcgctgtaagactaaatgaatcggttgaaaaagGCGGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGGATGCTGCTTGAGAGAGTGAGATTTACATTGGATGGCTTAGAATGTAATA---
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gtagatattaattttccagtgcatgtgatggaagattgagttattttctttgtgttcttggttgttttttgctgagagtttccttcttctcctattgaagGGTGGCC----CAGGTCAACCACAAAATTTGGGGGTCAATTTTTCTATGTGGATGCTGCTCGAGAGAGTGAGATTTACCTTAGATGGTCTTGAATGTAATAAAAMapped 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|116481172|gb|EG523764.1|EG523764EST: ACACAAGTATTCCTTCTTTCGAGGACTTCTATCTTGTAATCCCAAGAGAG GCGGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGG
genomic: ACACAAGTATTCCTTCTTTCGAGGACTTCTATCTTGTAATCCCAAGAGAGgtaactgctt ... gttgaaaaagGCGGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGG
EST:
gi|116481171|gb|EG523763.1|EG523763EST: ACACAAGTATTCCTTCTTTCGAGGACTTCTATCTTGTAATCCCAAGAGAG GCGGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGG
genomic: ACACAAGTATTCCTTCTTTCGAGGACTTCTATCTTGTAATCCCAAGAGAGgtaactgctt ... gttgaaaaagGCGGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaactcttttaacttgcaccgcgctgtaagactaaatgaatcggttgaaaaagGCGGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGGATGCTGCTTGAGAGAGTGAGATTTACATTGGATGGCTTAGAATGTAATA
gactaaa putative branch site (score: 2)
ttttaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactgcttatccatttgaactcttttaacttgcaccgcgctgtaagactaaatgaatcggttgaaaaagGCGGCTGAAGCGGGACAACCAGGGAGCTTAGGCGCAAATTACTCAATGTGGATGCTGCTTGAGAGAGTGAGATTTACATTGGATGGCTTAGAATGTAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT