Sequence
atgc intronic sequence ATGC exonic sequencegtatgcatgctagtagagtccattttcaccgccattggtggcttatctttttgttctgatttttattgtctgtaacattattgtttgacgacattgacattcaaacacatccctcttataaatttctaattttttcattgtttcaaatgcatttttattatgttccattcttcagCTGGATCCAGAGTTGGAATTTGATCGTGAGGTGTATCCCTTGGGACTTTTACCAAACGTGGGCGTCGTTGTTGGAGTTTCTCAGAGAATGTCATTTTCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61480.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61480.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 10
---------gtatgcatgctagtagagtc--cattttcaccgccattggtggcttatctttttgttctgatttttattgtctgtaacattattgtttgacgacattg-acattcaaacac----atccctctta---taaatttctaattttttcattgtttcaaatgcatttttattatg---ttccattcttcagCTGGATCCAGAGTTGGAATTTGATCGTGAGGTGTATCCCTTGGGACTTTTACCAAACGTGGGCGTCGTTGTTGGAGTTTCTCAGAGAATGTCATTTTCGG
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gtacagattttgtatcttgtgatagtattgacatctcttttgagttttgcgatccactctgtgaatttatcaattttttttggggaaaaacttgatcaaaatcataatagtttcatatgttgttttctttcttgcattgaactcttattggtggtagtattcaaagttaatggagaacatgctatttgtttctgcagCTGGATCCGGAGCTTGAATTTGACCGTGAGGTGTATCCGCTTGGTCTTCTTCCAAATGTTGGTGTAGTTGTTGGTATTTCTCAGAGAATGTCCTTCTCGA
upper sequence: AT3G61480.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 10
gtatgcatgctagtagagtccattttcacc--gccattggtggcttatctttttgttctgatttttattgtctgtaacat--tattgtttgacgacattgacattcaaacacatccctcttataaatttctaattttttcattgtttcaaatgcatttttattatgttccattcttcagCTGGATCCAGAGTTGGAATTTGATCGTGAGGTGTATCCCTTGGGACTTTTACCAAACGTGGGCGTCGTTGTTGGAGTTTCTCAGAGAATGTCATTTTCGG
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------------gtataagtctctgccatgagataattatgaatatccattataagttttgttacctttatgagaaacttgctgtagtcataatactttcatattctattcctcttctttaattcgttgaagacctcatgatgatgatattaacagctt-gtcatgtt--atactgtagTTGGACCCGGAGCTTGAGTTTGATCGTGAGGTGTATCCTCTTGGTCTTCTTCCAAATGTTGGTGTGGTTGTTGGTGTTTCTCAGAGAATGTCCTTCTCAA
upper sequence: AT3G61480.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 10
gtatgcatgctagtagagtccattttcaccgccattggtggcttatctttttgttctgatttttattgtctgtaacattattgtttgacgacattgacattcaaacacatccctcttataaatttctaattttttcattgtttcaaatgcatttttattatgttccattcttcagCTGGATCCAGAGTTGGAATTTGATCGTGAGGTGTATCCCTTGGGACTTTTACCAAACGTGGGCGTCGTTGTTGGAGTTTCTCAGAGAATGTCATTTTCGG
| | | | || | || ||| | || | | | | || | | || | | || || | | |||| || || |||||||||| ||| | || |||||||| ||||||||||| | || ||| | |||||||| || || |||||||| ||||| ||||| ||||| || ||
------------------------------------------------------------------------ctaaactttagtgaggggaaccaaacacctcctta-attcgttgaagacatcatgatgatattaacagccagttataaatgcatgtcatgtg--atactgtagCTGGATCCGGAGCTTGAGTTTGATCGCGAGGTGTATCCTCTTGGTCTTCTTCCAAACGTTGGTGTGGTTGTTGGTGTTTCCCAGAGGATGTCCTTCTCAA
upper sequence: AT3G61480.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 11
gtatgcatgctagtagagtccattttcaccgccattggtggcttatctttttgttctgatttttattgtctgtaacattattgtttgacgacattgacattcaaa-cacatccctcttataaatttctaattttttcattgtttcaaatgcatttttattatgttccattcttcagCTGGATCCAGAGTTGGAATTTGATCGTGAGGTGTATCCCTTGGGACTTTTACCAAACGTGGGCGTCGTTGTTGGAGTTTCTCAGAGAATGTCATTTTCGG
| ||| | | | || | | ||| | || || | | | | | ||| | || || ||| | | ||| | |||| || || ||||||| ||| |||| ||||||||||| || || || ||||||||| | ||||| | || || |||||||| ||||| ||||||||||||||| | |
------------------------------------------------------------------------ttacaat-tcatctggtggataggctatttgaggcaaataagttcagtcattccttcattctggaatcagtt--aatttactgaaattg-gcctcattttttagTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTGGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG
upper sequence: AT3G61480.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 11
gtatgcatgctagtagagtccattttcaccgccattggtggcttatctttttgttctgatttttattgtctgtaacattattgtttgacgacattgacattc-aaacacatccctcttataaatttctaattttttcattgtttcaaatgcatttttattatgttccattcttcagCTGGATCCAGAGTTGGAATTTGATCGTGAGGTGTATCCCTTGGGACTTTTACCAAACGTGGGCGTCGTTGTTGGAGTTTCTCAGAGAATGTCATTTTCGG
| ||| | | | || | | ||| || || || | | | | ||| | || | || ||| ||| ||| | |||| || || ||||||| ||| |||| ||||||||||| || || || ||||||||| | ||||| | || || |||||||| ||||| ||||||||||||||| | |
------------------------------------------------------------------------ttacaat-tcatctggtggataggctatttgaagcaaataaattcagtctttccttcattctggaatcgatt--aatttattgaaattg-gcctcattttttagTTGGATCCGGAGCTGGAGTTTGATCGTGAAGTATACCCTTTGGGACTTCTTCCAAATGCTGGTGTAGTTGTTGGTGTTTCCCAGAGAATGTCATTTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttctaattttttcattgtttcaaatgcatttttattatgttccattcttcagCTGGATCCAGAGTTGGAATTTGATCGTGAGGTGTATCCCTTGGGACTTTTACCAAACGTGGGCGTCGTTGTTGGAGTTTCTCAGAGAATGTCATTTTCGG
ttctaat putative branch site (score: 2)
ttccattcttc putative PPT
taattttttcattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcatgctagtagagtccattttcaccgccattggtggcttatctttttgttctgatttttattgtctgtaacattattgtttgacgacattgacattcaaacacatccctcttataaatttctaattttttcattgtttcaaatgcatttttattatgttccattcttcagCTGGATCCAGAGTTGGAATTTGATCGTGAGGTGTATCCCTTGGGACTTTTACCAAACGTGGGCGTCGTTGTTGGAGTTTCTCAGAGAATGTCATTTTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG