Sequence
atgc intronic sequence ATGC exonic sequencegttagaatttttccttgttgttccatgttataacttgcgcatgagagttctaagtgctaacaatgctgtcagcatcacatggttttgggaattcgtgatcaatttagcccatgtgctatcttacaaagaatagatgaacaggctttcaccattagattaacagtttctcttgtgtaaactgtagACTGAGTTTAAGAGAATCCAATCCCCACTGAAGTACCAGACGAGGTGTGTTACTGCCTTCCCTGATCAGCAAGGTTTTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G80670.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 6
gttagaatttttccttgttgttccatgttataacttgcgcatgagagttctaagtgctaacaatgctgtca-gcatcacatggttttgggaattcgtgatcaatttagcccatgtgctatcttacaaagaatagatgaacaggctttcaccattagattaacagtttctcttgtgtaaactgt-agACTGAGTTTAAGAGAATCCAATCCCCACTGAAGTACCAGACGAGGTGTGTTACTGCCTTCCCTGATCAGCAAGGTTTTTTG
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--------------------------------------------------------gtgattgtgttgttaagctgggcatgcatttgttgattcattttgagttagacattgatgacttct--------gttgtccaaatggcttatttcatgg------------cttctgtttgaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 6
gttagaatttttccttgttgttccatgttataacttgcgcatgagagttctaagtgctaacaatgctgtcagcatcacatggttttgggaattcgtgatcaatttagcccatgtgctatcttacaaagaatagatgaacaggctttcac--cattagattaacagttt--ctcttgtgtaaa---ctgtagACTGAGTTTAAGAGAATCCAATCCCCACTGAAGTACCAGACGAGGTGTGTTACTGCCTTCCCTGATCAGCAAGGTTTTTTG
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-----------------------------------------------------------------------------------------tactcgagttttattt--ctcaattaccagcagactcctggagaacatttggttcttcatttcattgcgtttcatgtctaaccatggttcaaataccaacagACTGAGTTTAAGAGAATCACTTCACCATTGAAGTATCAGACAAGATGTGTTGCTGCCTTTCCGGATCAGCAAGGATTCTTG
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 5
gttagaatttttccttgttgttccatgttataacttgcgcatgagagttctaagtgctaacaatgctgtcagcatcacatggttttgggaattcgtgatcaatttagcccatgtgctatcttacaaagaatagatgaacaggctttcaccattagattaacagtttctcttgtgtaaactgtagACTGAGTTTAAGAGAATCCAATCCCCACTGAAGTACCAGACGAGGTGTGTTACTGCCTTCCCTGATCAGCAAGGTTTTTTG
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-----------------------------------------------------------------------------gattgagtcaaggatctg-gttctttcta--ccatcatttgcacaccatttactagttctttata-ttctacttcaattctaataattatttaaataccaac---agACCGAGTTTAAGAGAATCACTTCACCCCTGAAGTATCAGACAAGATGTGTTGCAGCATTTCCTGATCAGCAAGGTTTCTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagatgaacaggctttcaccattagattaacagtttctcttgtgtaaactgtagACTGAGTTTAAGAGAATCCAATCCCCACTGAAGTACCAGACGAGGTGTGTTACTGCCTTCCCTGATCAGCAAGGTTTTTTG
gattaac putative branch site (score: 2)
attagattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaatttttccttgttgttccatgttataacttgcgcatgagagttctaagtgctaacaatgctgtcagcatcacatggttttgggaattcgtgatcaatttagcccatgtgctatcttacaaagaatagatgaacaggctttcaccattagattaacagtttctcttgtgtaaactgtagACTGAGTTTAAGAGAATCCAATCCCCACTGAAGTACCAGACGAGGTGTGTTACTGCCTTCCCTGATCAGCAAGGTTTTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG