Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39390.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC
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--------------------------------------------------------------tatcatagcagtgcagacctgatgttccc-ttgacttttacatattcc-ttacatgagcaaactg------------ggactaatgctttct---tcttcactcacttaatttc-----cagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
upper sequence: AT4G39390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 5
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC
|| || || || | | ||| | || |||| | | ||| ||| |||| | || | ||| || | ||||| | ||| | |||||||| | ||||| ||||||| || || ||||||||||| || ||||||||||| || || |||||||| || || || || |||||||| || || |
-------------------------------------------------------------------------tggaggat--atattttttataatctgttgttg--ccatgaccattact-atttttatcgtggcagggcctaacattttctttttttcatctacctgcatt------gtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAATTCATATGCATCGGAAGATTTACAGCAGTCTCGTTCCAAGTTCTAGGCC
upper sequence: AT4G39390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 5
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC
| | | | | | || |||| |||| | | | ||| ||| || ||| || ||| | |||| ||| ||| | |||||||| | | | ||||||| || || |||||||| ||||| ||||||||||| || || ||||||||||| || || || |||||||| || || |
-----------------------------------------------------------------------tatttgatctgcttgatgttataaattttcattc--ttcggcgcaaac-----ttgacgaacc----tgggcatgacttactattttcttatc--acatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC
upper sequence: AT4G39390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G31940.1 (Glycine max), 3'ss of exon 6
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC
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---------------------------------------------------------------gaaatcattttctattttgaatt-ccatatgcataggcctttgcctaatgttaac--tttacaatagtactatattgaactaatct-------gcttcttctg------ttt-----gcagTTGTTCATCATTATCTCTTGCACCATCGCAGTAGGGACAAACCTCAGCCAGTTCATCTGCATTGGCAGGTTCACGGCTGTATCTTTCCAAGTCCTTGGAC
upper sequence: AT4G39390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G15250.1 (Glycine max), 3'ss of exon 4
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacaca---attttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC
|| | | || || | | | | ||| | || || ||||| | ||||| | || | | |||| ||| | | |||||| ||| | || |||| |||| ||||| || ||||| || |||||||| |||||||| ||||| || ||||| || || ||||||||||| ||||| |
------------------------------------------------------------------------------------taatgaattttttttattttgaattc--cataagcattggcatttgcctaatgttg-acttgtcaatagtattattaaactaatcttcttattctgtttgcagTTGTTCATCATTATCTCCTGCACCATCGCAGTAGGGACAAACCTCAGCCAGTTCATCTGCATTGGCAGGTTCACAGCTGTATCTTTCCAAGTCCTTGGAC
upper sequence: AT4G39390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 5
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC
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-------------------------------------------------------------------------tatattcatttttctcatattcatgcatgttt-ttgcatcct----gctcgt-atcgtatcatttagga---atgctgctgatgatttgccccactttgttccctg--cagATGTTCATCATTCTGTCCTGCACAATTGCGGTAGGAACCAACCTCAGCCAATTCATCTGTATTGGAAGATTCACTGCAGTGTCCTTCCAAGTGATTGGGCMapped 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|86079696|gb|DR375453.1|DR375453EST: GGTTGACTAACCAAAGAGTGGATGCATACAACTTTTCATTTGTATCTCTG TTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAA
genomic: GGTTGACTAACCAAAGAGTGGATGCATACAACTTTTCATTTGTATCTCTGgtaaagtttc ... ttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC
atctaac putative branch site (score: 2)
tttttt putative PPT
taacacaatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC
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