Sequence
atgc intronic sequence ATGC exonic sequencegtaatattttcttctgtattatggtaatcctgaatcttttcttctttttcgtttgttgtatgcttatgctctttttgtctgttggaagAAACTGTTCCCATCAGAACCGTGAACAGACAGTGTTCATCTGGGCTTCAGGCTGTTGCTGATGTTGCCGCTGCCATAAAAGCTGGTTTTTATGACATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04710.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G848768_T02 (Zea mays), 3'ss of exon 4
-----------------------gtaatattttcttctgtattatggtaatcctgaatcttttcttctttttcgtttg------ttgtatgcttatgctctttttgt-----ctgttg--gaagAAACTGTTCCCATCAGAACCGTGAACAGACAGTGTTCATCTGGGCTTCAGGCTGTTGCTGATGTTGCCGCTGCCATAAAAGCTGGTTTTTATGACATTG
| || | || | || |||| | || || | |||||| | || | |||| || ||||| | |||||| || || | ||||| || ||| | ||||||||||||||||| ||||| || |||||||| || ||||| ||||| ||||||| |||||||| |
gtaactgataactgttgtttacgatcatgcatgctacc-taatatgaagaagacga-tcctatcttctggtggacaaaaaaagaagagataatgatgcatcccatgatgatgttgttgttgcagAAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAG
upper sequence: AT1G04710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 4
gtaatattttcttctgtatt-atggtaatcctgaatcttttct-tctttttcgtttgttgt--atgcttatgctctttttgtctgttggaagAAACTGTTCCCATCAGAACCGTGAACAGACAGTGTTCATCTGGGCTTCAGGCTGTTGCTGATGTTGCCGCTGCCATAAAAGCTGGTTTTTATGACATTG
||| || | | || || || | ||||| || | | | | | ||||||| | || ||| || | || || || ||||||||| || | || || || || || || |||||||||||||| ||||||||||||||||| || ||||| |||| ||||| || ||||||||||
gtatgtttagaatttagatagattgtgcttctgaacctgatatatgatctgggtttgttatttatacttgtgatgttattttcatcc---agAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG
upper sequence: AT1G04710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G24590.3 (Glycine max), 3'ss of exon 4
gtaatattttcttctgtattatg-gtaatcctgaatcttttct-tctttttcgtttgttgtatgcttatgctctttttgtctgttggaagAAACTGTTCCCATCAGAACCGTGAACAGACAGTGTTCATCTGGGCTTCAGGCTGTTGCTGATGTTGCCGCTGCCATAAAAGCTGGTTTTTATGACATTG
||| | | | || | || | | || || || | | || ||||| | | | ||| | | || | | ||||||||| || | || ||||| || || || |||||||||||||| |||||||| |||||||| || ||||| |||| ||||| || ||||||||||
gtatgtctagaatttagatagtttgtgcttgtaaacctgttatatgattcgggtttggtatttatacatg-tgatgttattttcatccagAAACTGTGCCTGTTAGGACCGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTCGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG
upper sequence: AT1G04710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0051g00720.t01 (Vitis vinifera), 3'ss of exon 4
gtaatattttcttctgtattatggtaatcctgaatcttttcttctttttcgtttgttgtatgcttatgctctttttgtctgttggaagAAACTGTTCCCATCAGAACCGTGAACAGACAGTGTTCATCTGGGCTTCAGGCTGTTGCTGATGTTGCCGCTGCCATAAAAGCTGGTTTTTATGACATTG
||| || || | ||| | | | | | | || | || |||| | || | | | ||| | | ||||||||| || ||||||| |||||||| || ||||||||||| |||||||| ||||||||||| || ||||| || |||||||| |||||||||||||
---gtatatttccttgaactatcct--ttatatttttggttttgtacccatttcattgttcacaaatattatatctgt--gatttcagAAACTGTGCCTGTCAGAACTGTGAACAGGCAATGTTCATCTGGTCTTCAGGCAGTTGCTGATGTAGCTGCTGCAATTAAAGCTGGGTTTTATGACATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttttcttctttttcgtttgttgtatgcttatgctctttttgtctgttggaagAAACTGTTCCCATCAGAACCGTGAACAGACAGTGTTCATCTGGGCTTCAGGCTGTTGCTGATGTTGCCGCTGCCATAAAAGCTGGTTTTTATGACATTG
ctctttttgtctgtt CT-rich tract
ttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatattttcttctgtattatggtaatcctgaatcttttcttctttttcgtttgttgtatgcttatgctctttttgtctgttggaagAAACTGTTCCCATCAGAACCGTGAACAGACAGTGTTCATCTGGGCTTCAGGCTGTTGCTGATGTTGCCGCTGCCATAAAAGCTGGTTTTTATGACATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG