Sequence
atgc intronic sequence ATGC exonic sequencegttgagacatctcaatcctcttgtttggttcacatgagtccaaaatatgatatagcttgtttggttcacatgagtccaaaatatgatatagcttcctaaccatttttggaactttttcagCCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGGTTGTATGAGATCTGATAAAGGCCCCTGGAATGACCCTGAGATATTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G75370.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 6
gttgagacatctcaatcctcttgtttggttcacatg-agtccaaaatatgatatagcttgtttggttcacatgagtccaaaatatgatatagcttcctaaccatttttggaactttttcagCCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGGTTGTATGAGATCTGATAAAGGCCCCTGGAATGACCCTGAGATATTAAAG
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-----------------------gtaactctacattcaattctgttaatggagt--tttctctcaatcaactagtttagttatttgaaaattctgactaactgt-------aagttctcagTGAGCTGCCAGAATTTCTTGGTGGCAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 7
gttgagacatctcaatcctcttgtttggttcacatgagtccaaaatatgatatagcttgtttggttcac--atgagtccaaaatatgatatagct-tcctaaccatttttggaactttttcagCCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGGTTGTATGAGATCTGATAAAGGCCCCTGGAATGACCCTGAGATATTAAAG
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-------------------------------gtaactatgcaataatttttgttaatggcgttatttatcaatcagtttgtattgttatttggaaattctgactatctgcgtgg-tttttcagCGAGCTGCCTGAATTTCTAGGTGGTAATTGCACTTGTATGGATCGAGGTGGTTGTATGAGATCTGATAAAGGGCCATGGCAGGATCCAAACATTTTAAAG
upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 7
gttgagacatctcaatcctcttgtttggttcacatgagtccaaaatatgatatagcttgtttggttcacatgagtccaaaatatgatat-agcttcctaaccatttttggaactttttcagCCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGGTTGTATGAGATCTGATAAAGGCCCCTGGAATGACCCTGAGATATTAAAG
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----------------------------gtaacactacattcaattctgttaacggagttttctctca-atcaactagttttgttatttgaaaattctaactaaccgtaag---ttctcagTGAGCTGCCAGAATTTCTTGCTGGTAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
upper sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 7
gttgagacatctcaatcctcttgtttggttcacatgagtccaaaata-tgatatagcttgtttggttcaca-tgagtccaaaatatgatatagct-tcctaaccatttttggaactttttcagCCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGGTTGTATGAGATCTGATAAAGGCCCCTGGAATGACCCTGAGATATTAAAG
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-----------------------gtaactatgcattaatttttgttaatggtgttatttacttatttatcaatcagcttgtattgttatttggaaattctgactatctgcgtggtttgtttagCAAGCTGCCTGAATTTCTAGGTGGTAGTTGCACTTGTATAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAGGATCCAAACATTTTAAAGMapped 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|164033578|gb|ES040862.1|ES040862EST: AGTACCAAAACAAACTACTTGAGATCATTGATGCAAG CCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGG
genomic: AGTACCAAAACAAACTACTTGAGATCATTGATGCAAGgttgagacat ... actttttcagCCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGG
EST:
gi|124741856|gb|EH833018.1|EH833018EST: GTCATTGGTAACAAGTACCAAAACAAACTACTTGAGATCATTGATGCAAG CCAGCTGCCAGATTTT
genomic: GTCATTGGTAACAAGTACCAAAACAAACTACTTGAGATCATTGATGCAAGgttgagacat ... actttttcagCCAGCTGCCAGATTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacatgagtccaaaatatgatatagcttcctaaccatttttggaactttttcagCCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGGTTGTATGAGATCTGATAAAGGCCCCTGGAATGACCCTGAGATATTAAAG
tcctaac putative branch site (score: 1)
ctttttc putative PPT
aaaatatgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgagacatctcaatcctcttgtttggttcacatgagtccaaaatatgatatagcttgtttggttcacatgagtccaaaatatgatatagcttcctaaccatttttggaactttttcagCCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGGTTGTATGAGATCTGATAAAGGCCCCTGGAATGACCCTGAGATATTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC