Sequence
atgc intronic sequence ATGC exonic sequencegtaattttctatcgtttgatcttgagtgttcaaatctacatacttgctgtccatacgtagtattgttgaagtaatcatttggtttccctaatttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13300.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 8
gtaattttctatcgtttgatcttgagtgttcaaatctacatacttgctgtccatacgtagtattgttgaagtaatcatttggtttccctaatttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
| | | |||| | || | | ||| | ||||| | | | | |||| || ||| || || |||||||||||| || |||||| | || || |||||||| ||||||||||| || || |||||||| ||||||||||||||||| || || ||||||||
----------------gtacatgcactgtttccctgtataactgttctgatt-tctgtagttgtat-gtaccgtggctttgtcttatctatttaattttcagGTGACTGCACTTTCAAATATCGAGGCCAAGAAAAGATTTGAATTTTTAGAGGCTGTCAGTGGGACAATGGATGCACATCTGCGCTATTTCAAACAA
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 8
gtaattttctatcgtttgatcttgagtgttcaaatctacatacttgctgtccatacgtagtattgttgaagtaatcatttggtttcccta-atttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
|| | | | || ||| ||| || || | | || | ||| || || | |||| | | | || | || || |||||| |||||||||||| || |||||| | || |||||||||||||||||||||||||| || || ||||| ||||||||||| |||||||| || ||||||||
--------gta-cataccctgtttagttgtcacttc-actt-catgat-tccttattta-cacagttggaatg--ccttcgtcttatctgtatttatattcagGTGACTGCACTTTCAAATATCGAGGCTAAGAAAAGGTTTGAATTTTTGGAGGCTGTTAGTGGGACAATGGATGCTCATCTTCGTTATTTCAAACAA
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 8
gtaattttctatcgtttgatcttgagtgttcaaatctacatacttgctgtccatacgtagtattgttgaagtaatcatttggtttccctaatttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
|| | | | | ||||||| ||| |||| | || | | |||| || || || ||| | | || | || ||||| ||||| | |||||||||||||| ||||| || |||||||||||||||||||||||||| || ||||||||||||||||| ||||||||||||
gttagtaaat-taatttgatcagaagtacataaataattactgttaccatgcatatgt----tttcacaaataaactcgaagagtcttt------tgtccagGTTACTGCCTTGTCAAATGTTGAAGCAAAGAAGAGATTTGAATTTTTGGAAGCAGTCAGTGGGACCATGGATGCACATCTTCGTTACTTCAAACAG
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 8
gtaattttctatcgtttgatcttgagtgttcaaatctacatacttgctgtccatacgtagtattgttgaagtaatcatttggtttccctaatttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
|| | | | || ||||||| || ||||| || ||| | | || || || || ||| | | || | | ||||| ||||| | |||||||||||||| ||||| || |||||||||||||||||||||||||| || ||||||||||||||||| ||||||||||||
gttagtaaat-tcatttgatcagaagca--caaata---attattgttaccatgacatatgttttcacaaataaactcgaagagtctttggtc------cagGTTACTGCCTTGTCAAATGTTGAAGCAAAGAAGAGATTTGAATTTTTGGAAGCAGTCAGTGGGACCATGGATGCACATCTTCGTTACTTCAAACAG
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 8
-------------------gtaattttctat---cgtttg--atcttgagtgttcaaatctacatacttgctgtccatacgtagtattgttgaagt--aatcatttggtttccctaat-ttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
|||| |||||| | ||| | ||||| | | || |||| ||| | | | | | || | | | | | ||| ||| || || ||||| ||| |||| || ||||||||||| || |||||||| ||||| ||||||||||| ||||| ||||||||||| || ||||| |||||||| |||
gtatgtacgattcttgcaattaatgttctatgcatgattgtcaacttgaatttccagatctggata-tggatattatggtgccaagttaataacatctgagcttttataacttggaatattctgtccagGTAACTACTCTTTCTAATGTTGAAGCAAAAAAAAGGTTCGAATTCTTGGAAGCAGTTAGTGGGACAATGGATGCTCACCTTCGCTACTTCAAGCAG
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ24732 (Selaginella moellendorffii), 3'ss of exon 8
gtaattttctatcgtttgatcttgagtgttcaaatctacatacttgctgtccatacgtagtattgttgaagtaatcatttggtttccctaatttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
|| | ||| || || | | ||| | | || | ||| | |||||| || || || || || |||| || || || | |||||| || | ||||| |||||||| ||||||||||||||||||| |||||||| |||
-----------------------------------------gtatgttttccccgtttattagcga-ggagttttaagctg-------tggtttgta-tcagGTTACAGCACTGTCGAACATTGAGGCCAAAAAGAAGTTTGAGTTCCTAGAAGCCGTCAGTGGCTCAATGGATGCACATCTTCGATACTTCAAGCAG
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ08060 (Selaginella moellendorffii), 3'ss of exon 8
gtaattttctatcgtttgatcttgagtgttcaaatctacatacttgctgtccatacgtagtattgttgaagtaatcatttggtttccctaatttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
|| | ||| || || | || | | | | | | || | |||||| || || || || || |||| || || || | |||||| || | ||||| |||||||| ||||||||||||||||||| |||||||| |||
-----------------------------------------gtatgttttccccgtttattagcg----aggagttttaagctgt-----ggttgta-tcagGTTACAGCACTGTCGAACATTGAGGCCAAAAAGAAGTTTGAGTTCCTAGAAGCCGTCAGTGGCTCAATGGATGCACATCTTCGATACTTCAAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtccatacgtagtattgttgaagtaatcatttggtttccctaatttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
ccctaat putative branch site (score: 3)
taatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattttctatcgtttgatcttgagtgttcaaatctacatacttgctgtccatacgtagtattgttgaagtaatcatttggtttccctaatttatgctcagGTGACTGCTCTATCAAATGTTGAAGCTAAGAAAAGGTTTGAATTTTTGGAAGCAGTCAGTGGAACAATGGATGCACATCTTCGGTACTTCAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA