Sequence
atgc intronic sequence ATGC exonic sequencegttcgatagtaaaccaactcccacatgagaaaaaccaacaaagtctcctttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34660.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 9
gttcgatagtaaaccaactcccacatgagaaaaaccaacaaagtctcctttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtca---ttgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
|| | | || || ||| || | || || | || || || | || || | | | ||| | | | | | | | ||| | ||||| || || ||||||||| ||||||||||||| ||| |||||||| ||||||||||| | ||||| || | | |||| || || ||||| || ||||
-----gtacggccctatcttcc-cattggacatgtttctaa-----ccataaacatatctttgctgg-acttttgtg-ggcaaagttggctacactaaacttgtgttcattaacctgctcaatcagGTGTCAAACAATGGATGGGCAGAAGGTGAATGCAGAGGGAAAGCTGGCTGGTTCCCTTACGACTACATCGAGAAAAGGGACCGTGTGCTTGCAAGTAAAG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
------------------------------------------------------gttcgatagtaaaccaactcccacatgagaaaaaccaacaaagtctcc-tttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
||| | | || ||||| || | | | | | ||| ||| || | | | | || | ||| | | | || | ||||| | || ||||||||||||||||||||||| || ||||||||||||||||| || | ||||| || | |||||| || || ||||| || ||||
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctt-----tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G104166_T01 (Zea mays), 3'ss of exon 4
gttcgatagtaaaccaactcccacatgagaaaaaccaacaaagtctcctttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgc-cagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
| | |||| | || || ||| || ||| || | | | | | |||| || | ||||| || | ||| | || ||| ||| ||||| |||||||||||||| |||||||| || ||||||||| ||| || || ||||| | |||||| ||||| || |||||||
--------------------tgggttctgtaaaatgattaa----tcatttttgccagcagctccattaagaatgtgtatgatcatttggcctgcatttgtcctctcttttctctgaaacacagATCTCAAGCAATGGTTGGGCAGAAGGTGAATGCAAGGGCAAAGCAGGATGGTTCCCTCATGCTTATATCGAAAGGCAGGAACGTGTTCTAGCAAGCAAAG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 9
---gttcgatagtaaaccaactcccacatgagaaaaaccaacaaagt--ctcctttaattcatat-taaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
|| | | | ||| || | | | | || | || ||| ||| || | | | | | | || | ||| || || | || | ||| | | | || | ||||| | || ||||||||||||||||||||||| || | |||||| |||||||| || | ||||| || | ||| || || || ||||| || ||||
gtagtgctttctcatacctgctgcggccagcttcacacagatttggttgctcattttatgagtgtctcaatcacattgt-actcaaacttgattactgaattt--cacataaaaaactttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGGTTCCCCTACGACTACATCGAGAAACGAGAGCGTGTGCTTGCAAGTAAAG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 9
gttcgatagtaaaccaactcccacatgagaaaaaccaacaaagtctcctttaattcatattaaccaatacggttattcagtagtgtttgtttgatat-accacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
||| ||||| ||| | | | | | ||| || | | | | ||| | || | | | | | |||| ||||| ||| || ||||||||| || |||||||||||||| ||||| |||||||| || | ||| |||||||||||| |||| ||||| || || ||||| |
-----------------------catatttaaaacaaacttttggttgtggtggtagtggggatggataaccctaaa-atcattacatattttaaattgttcccaatatgactctgattggcagGTGACAAACAATGGATGGGCTGAGGGTGAATGCAAAGGGAAAGCAGGTTGGTTTCCATTTGGTTACATTGAAAGAAGGGAGCGAGTCCTCGCAAGCAAGG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 9
gttcgatagtaaaccaactccca--catgagaaaaaccaacaaagtctcctttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
|||| |||| || | | | | | | |||| || || ||| ||||| | |||| |||| | || | | ||| || ||||| ||| || ||||||||| || |||||||||||||| ||||| |||||||| || | ||| ||||| |||||| |||| ||||| || || ||||| |
---------aaaacaaacttttggttgtggtgatagtgggaacggattaccttaa--------aatcattaca--tattctaaattgttc--ccaatatgactctgattgaattgaca----cagGTGACAAACAATGGATGGGCTGAGGGTGAATGCAAAGGGAAAGCAGGTTGGTTTCCATTTGGTTACATAGAAAGAAGGGAGCGAGTCCTCGCAAGCAAGG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 9
--------------------------------gttcgatagtaaaccaactc-----ccacatgagaaaaaccaa-caaagtctcctttaattcatattaaccaatacgg-----------ttattcagtagtgtttgtttga------tataccacttctctatttgtca-----ttgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
|| | | |||||| || || | ||| |||||| | | | ||| | | | | |||| | || ||| | || | ||| | | ||| | | | | || || ||||| ||| ||||||||||||||| |||||||||||||||| || |||||||| || | | | ||||||||| | |||| || |||||||| ||||| |
gttcgtagctttctgcatctgaatataattatattttacgatgaaccaattcaaaactgacgcgggaataaccaagtagaatgcatttttaccattgtcatgcaatgctaacaaaaaatccttgttcttcaagtttgatctgattttcctttgccattattatggtggttgtggttttaacagGTGACAAACAGTGGATGGGCCGAGGGTGAATGCAAAGGCAGGGCAGGTTGGTTTCCGTTTAGTTACATTGAACGGAGGGAGCGGGTTCTTGCGAGCAAGG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 8
--------------------------------gttcgatagtaaaccaactc-----ccacatgagaaaaaccaacaaagtctcctttaattcat-attaaccaatacggttattcagtagt----------gtttgtttgatataccacttctctatttgtcat-----------tgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
|| | | ||||| || ||| | ||| |||||| | | |||| ||| || | |||| | || | | | ||| | |||| | || | | | || | | | ||||| ||| ||| ||||||||||| |||||||||||||||| || |||||||| || | | | ||||||||| | |||| || |||||||| ||||| |
gttaatagttttctgcatctgaatataactatattttacgatgaaccatttcaaaactgacacgggaataaccaagtagaatgcatttataccattatcatgcaatgctaacataaaatccttgttttccaagttgatctgattttcctttgccattattatggtgcttacggttttaacagGTGACAAACAGCGGATGGGCCGAGGGTGAATGCAAAGGCAGGGCAGGTTGGTTTCCGTTTAGTTACATTGAACGGAGGGAGCGGGTTCTTGCGAGCAAGG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 9
gttcgatagtaaaccaactcccacatgagaaaaaccaacaaagtctcctttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
|| || ||| | || || | | ||| | | ||| | | | || ||| | |||| ||| | | ||||| ||| |||| | | ||||||||| ||||||||||||||||| || || ||||||||||| | ||| || |||||| |||||||| |||||||| |||||
-----------cttcactgttcagctgaaaccaatgggcacacggttgtttg-tcttttttatttatttggaccatgttgtaatagc-gtttcatac------tttatattt----ttggtagGTGTCTAATAATGGATGGGCTGAAGGTGAATGCAAAGGAAAGGCAGGTTGGTTCCCATTTGGATATGTTGAAAAGCGGGAACGGGTTCTTGCAAGCAAGA
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 9
gttcgatagtaaaccaactcccacatg-agaaaaaccaacaaagtctcctttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
|| || || | | | | | ||| || ||| || | |||| | ||| ||| | | | ||| || | ||| ||| ||||| || |||||| ||||| ||||||||||||| ||| ||||| ||||||||||| ||| ||||| |||||||| ||||| |||||||| |||||
-------------------cctttttgcagtatatcttgcttattcttagcatgtttggatttggttat-cttttatccca----gttcttttacgagatctgttcactttctgtgcttggcagGTGTCAAACAGTGGCTGGGCAGAAGGTGAATGCAGAGGAAAAGCAGGTTGGTTCCCAGTTGGATACATAGAAAGACGAGAACGCGTTCTTGCAAGCAAGTMapped 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|86079177|gb|DR374934.1|DR374934EST: CAGATGTCGAGCTCAGCTTATCAACTGGTGAATACGTTGTTGTTAGAAAG GTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGG
genomic: CAGATGTCGAGCTCAGCTTATCAACTGGTGAATACGTTGTTGTTAGAAAGgttcgatagt ... tcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
gtttgat putative branch site (score: 5)
cttctctatttgtc putative PPT
tttgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgatagtaaaccaactcccacatgagaaaaaccaacaaagtctcctttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG