Sequence
atgc intronic sequence ATGC exonic sequencegtaatggtggatttcctggagttatctctgaccaatctgttccgaaattagagttttaagctgttttatttgatttttctttgggattgtatttgcagCTTCCTGATTATCATGATATGATAGAGCATCCCATGGATTTTTCCACAGTGAGGAAGAAGCTTGCGAATGGATCATATTCTACGTTGGAAGAGCTCGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55040.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G05000.1 (Glycine max), 3'ss of exon 5
gtaatggtggatttcctggagttatctctgaccaatctgttccgaaattagagttttaagctgttttatttgatttttctttgggattgtatttgcagCTTCCTGATTATCATGATATGATAGAGCATCCCATGGATTTTTCCACAGTGAGGAAGAAGCTTGCGAATGGATCATATTCTACGTTGGAAGAGCTCGAG
|| || || ||| | | | | | || | | ||| || || | ||| | ||| | | ||||||||||||||||||||||| |||| |||||||||||||| ||| |||| |||||||||||| | | |||||||| ||| |||| || ||| | | |||
gtg-tgttgatttttattcctgtgagttggtaaatcttgcttttgga--agacacccgagttggaagttcaaattctgtttttg------acatgcagCTTCCTGATTATCATGATGTGATCGAGCATCCCATGGACTTTGCCACTGTGAGGAAGAAGTTGGGAAATGGATCTTATACTACCTTAGAACAATTTGAG
upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G10850.1 (Glycine max), 3'ss of exon 4
gtaatggtggatttcctggagttatctctgaccaatctgttccgaaattagagttttaagctgttttatttgatttttctttgggattgtatttgcagCTTCCTGATTATCATGATATGATAGAGCATCCCATGGATTTTTCCACAGTGAGGAAGAAGCTTGCGAATGGATCATATTCTACGTTGGAAGAGCTCGAG
|| || | ||| || | | | | || | | | | | || || | ||| | ||| | | ||||||||||||||||||| |||| |||| |||||||||||||| ||| |||| |||||||||||| | | |||||||| ||| |||| || ||| | | |||
gtg-tgtcgatttttcttcctgtgagttggtaaatcttgcttttggaagacacccctgagttggaagttcaaattctgtttttg------acttgcagCTTCCTGATTATCTTGATGTGATCGAGCATCCCATGGACTTTGCCACTGTGAGGAAGAAGTTGGGAAATGGATCTTATACTACCTTAGAACAATTTGAG
upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G43050.1 (Glycine max), 3'ss of exon 4
gtaatg-gtggatttcctggagttatctctgaccaatct-gttccgaaattagagttttaagctgttttatttgatttttctttgggattgtatttgcagCTTCCTGATTATCATGATATGATAGAGCATCCCATGGATTTTTCCACAGTGAGGAAGAAGCTTGCGAATGGATCATATTCTACGTTGGAAGAGCTCGAG
|| || ||||| | || ||||| | | | | | | || || | ||| | ||| | | ||||||||||||||||||||||| |||| |||||||||||||| ||| | || |||||||||||| | | |||||||| ||| |||| || ||| | | |||
---gtgcgtcgatttttcttcctgtgagttggtaaatcttgcttttggaagacacccctgagttggaagttcaaattctgtttttg------acatgcagCTTCCTGATTATCATGATGTGATTGAGCATCCCATGGACTTTGCTACTGTGAGGAAGAAGTTGGGAAATGGATCTTATACTACCTTAGAACAATTTGAG
upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G10890.1 (Glycine max), 3'ss of exon 3
gtaatggtggatttcctggagttatctctgaccaatctgttccgaaattagagtttt-aagctgttttatttga---tttttctttgggattgtatttgcagCTTCCTGATTATCATGATATGATAGAGCATCCCATGGATTTTTCCACAGTGAGGAAGAAGCTTGCGAATGGATCATATT---CTACGTTGGAAGAGCTCGAG
| | || |||| | | || | ||| || | | ||| ||| | | ||| ||| || | || | || |||||||||||||||| ||| |||| ||||||||||||| ||| |||| |||||||||||| | | |||| ||| | || |||| || ||| | | |
-----------gtgtgtcgaattattttt--cctgtgagttgttaatcttgcttttggaagacacctgagttggaagtttaaattctgtttttgacatgtagCTTCCTGATTATCACGATGTGATCAAGCATCCCATGGACTTTGCCACTGTGAGGAAGAAGTTGGGAAATGAATCTTCTTATACTACCTTAGAACAATTTG--
upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0090g00610.t01 (Vitis vinifera), 3'ss of exon 4
gtaatggtggatttcctggagttatctctgaccaatctgttccgaaattagagttttaagctgttttatttgatttttctttgggattgtatttgcagCTTCCTGATTATCATGATATGATAGAGCATCCCATGGATTTTTCCACAGTGAGGAAGAAGCTTGCGAATGGATCATATTCTACGTTGGAAGAGCTCGAG
| || | | ||||| | || | || || || | | || || | | | ||| | | || || |||| ||||||||||||||| |||| |||||||| ||||| || | |||||||||||||| |||| |||||| |||||| ||| || || || | |||
-----------gtgtttgaaatactctcttaatttgctttatgtaatttgaagacattatttgcattgga-gtctataacttgtgttggttcttatagCTGCCTGATTATCATGATGTGATTGAGCATCCAATGGACTTCGCGACAGTGAGGAAGAAACTTGGGAATGGGTCATATCGTACCTTTGAGGAATTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaattagagttttaagctgttttatttgatttttctttgggattgtatttgcagCTTCCTGATTATCATGATATGATAGAGCATCCCATGGATTTTTCCACAGTGAGGAAGAAGCTTGCGAATGGATCATATTCTACGTTGGAAGAGCTCGAG
atttgat putative branch site (score: 5)
tgttttatttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggtggatttcctggagttatctctgaccaatctgttccgaaattagagttttaagctgttttatttgatttttctttgggattgtatttgcagCTTCCTGATTATCATGATATGATAGAGCATCCCATGGATTTTTCCACAGTGAGGAAGAAGCTTGCGAATGGATCATATTCTACGTTGGAAGAGCTCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT