Sequence
atgc intronic sequence ATGC exonic sequencegtgagctcctaaaccaaagactaacccgaggtttagccaatgcaacttcaaatttttctgcatcacgtattattaacaccatgatatctgatattgtgtgcagGGATATCACAACTACATTTCCGAGCTTTGTGTTACACTCGCAAGTGGAAGATACCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26560.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 8
--------gtgagctcctaaaccaaagactaacccgaggtttagccaatgcaacttcaaatttttctgcatcacgtattattaacaccatgatatctgatattgtgtgcagGGATATCACAACTACATTTCCGAGCTTTGTGTTACACTCGCAAGTGGAAGATACCTGA------------------------------------------
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aaaaaagattaggtgttcataaaaatgttcaagtctataaaaatgttgtagacacttttgtttttctatagcacaagctaatcttgccaca-----------tgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC
upper sequence: AT4G26560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
-gtgagctcctaaaccaaagactaacccgaggtttagccaatgcaacttcaaatttttctgcatcacgtattattaacaccatgatatctgatattgtgtgcagGGATATCACAACTACATTTCCGAGCTTTGTGTTACACTCGCAAGTGGAAGATACCTGA------------------------------------------
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gatttagtctggatactttttttcttcctattttacttcgattgctctttgg-ttactccatttcacagacc-taagtacctaaccatatca-actttg-gcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAATCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT
upper sequence: AT4G26560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
---------------------------------------------------------------------------------------gtgagctcctaa-accaaagactaacccga--ggtttagccaatgcaacttcaaatttttctgcatcacgtattattaacaccatgatatctgata-ttgtgtgcagGGATATCACAACTACATTTCCGAGCTTTGTGTTACACTCGCAAGTGGAAGATACCTGA------------------------------------------
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gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagt-attgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaatttttctgcatcacgtattattaacaccatgatatctgatattgtgtgcagGGATATCACAACTACATTTCCGAGCTTTGTGTTACACTCGCAAGTGGAAGATACCTGA
tattattaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctcctaaaccaaagactaacccgaggtttagccaatgcaacttcaaatttttctgcatcacgtattattaacaccatgatatctgatattgtgtgcagGGATATCACAACTACATTTCCGAGCTTTGTGTTACACTCGCAAGTGGAAGATACCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA