Sequence
atgc intronic sequence ATGC exonic sequencegtaataatggaatataaccatacacttaacagaacagaatttctattcaaactctagaatcagattgaatatgctgtgcttctaatgagatgtctcttgctgtccctagGTCCTGATCAGCGGAATACTGCAAATGCTGTGTTCTGCTTGTGGATGGCTATTGGGAACATCCTTGGGTTTTCTGCCGGTGCTAGCGGAAAATGGCAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G02860.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G02860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G145107_T01 (Zea mays), 3'ss of exon 6
gtaataatggaatataaccatacacttaacagaacagaatttctattcaaactctagaatcagattgaatatgctgtgcttctaatgagatgtctcttgctgtccctagGTCCTGATCAGCGGAATACTGCAAATGCTGTGTTCTGCTTGTGGATGGCTATTGGGAACATCCTTGGGTTTTCTGCCGGTGCTAGCGGAAAATGGCAAGA
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-------------gtggttactatcttaa--gtttagaaagtttact--aatgctgtattca--tcaagtgt--tagttattcaatga--tcctttctattatgc--agGTCCTGATCAGTGCAATTCTGCAAATGCAATATTCTGCTCATGGATGGCTGTTGGGAATATTCTTGGTTTTTCAGCTGGAGCGAGTGGGGAATGGCACAA
upper sequence: AT2G02860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G15950.1 (Glycine max), 3'ss of exon 6
-------------------------------gtaataatggaatataaccatacacttaacagaacagaatttc-tattcaaactctagaatcagattgaatatgctgtgc--ttctaatgagatgtctcttgctgtccctagGTCCTGATCAGCGGAATACTGCAAATGCTGTGTTCTGCTTGTGGATGGCTATTGGGAACATCCTTGGGTTTTCTGCCGGTGCTAGCGGAAAATGGCAAGA
|| ||| | ||||| || | | | || |||| |||| || | | | | ||| || | || | | | || | | | | ||||||||||||| || ||| |||||||||||| || |||| ||||||||| ||||||||||||| || | |||| | |||||||| ||||| ||| | |
gtaaagcttggctgtctcacttgtttttcttgttcaaattctcaacaacca--caatcgggattattgattttcatatttaa--ttaaatacttgtttggtagtgaggagccatcatggtttaataagtttgcttctatttagGTCCTGATCAACGCAATGTTGCAAATGCTGTATTTTGCTCGTGGATGGCAGTTGGGAACATCCTAGGATATTCTTCAGGTGCTAGTGGAAAGTGGAACAA
upper sequence: AT2G02860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G40980.1 (Glycine max), 3'ss of exon 6
----------------gtaataatggaatataaccatacacttaacagaacagaatttctatt-caaactctagaatcagattgaata-tgctgtgcttctaatgagatgtc------------tcttgctg-tccctagGTCCTGATCAGCGGAATACTGCAAATGCTGTGTTCTGCTTGTGGATGGCTATTGGGAACATCCTTGGGTTTTCTGCCGGTGCTAGCGGAAAATGGCAAGA
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gtaaagcttgctggtctcacttgttttttttgttcaaattctcagca-accacaatggggattgttgattttcatatttaattaaatacttgtttggtagtgaggagccatcgcagtttaataattttgcttctatttagGTCCTGATCAACGCAATGTTGCAAATGCTATATTTTGCTCGTGGATGGCAGTTGGGAACATCCTAGGATATTCTTCAGGTGCTAGTGGAAAGTGGAACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaatcagattgaatatgctgtgcttctaatgagatgtctcttgctgtccctagGTCCTGATCAGCGGAATACTGCAAATGCTGTGTTCTGCTTGTGGATGGCTATTGGGAACATCCTTGGGTTTTCTGCCGGTGCTAGCGGAAAATGGCAAGA
ttctaat putative branch site (score: 2)
tctcttgctgtccct putative PPT
attgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataatggaatataaccatacacttaacagaacagaatttctattcaaactctagaatcagattgaatatgctgtgcttctaatgagatgtctcttgctgtccctagGTCCTGATCAGCGGAATACTGCAAATGCTGTGTTCTGCTTGTGGATGGCTATTGGGAACATCCTTGGGTTTTCTGCCGGTGCTAGCGGAAAATGGCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA