Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcaactcgtacttacatttaaactaaaacctggtttgatatgcttgcctcatttccatgtaaaactctttacatttctctgcgcagGTGGCTTGGCAAGATCACTTTAGAGACTTACATTTCCCAGTTTCATATATGGCTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46340.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 12
gtgagtcaactcgtacttacatttaaactaaaacctggtttgatatgcttgcctcatttccatgtaaaactctttacatttctctgcgcagGTGGCTTGGCAAGATCACTTTAGAGACTTACATTTCCCAGTTTCATATATGGCTAAG
| || || || ||| | | | ||| | | | || | |||| ||| | | | | || | | || ||||||||||||||||| ||||||| |||||||||||| |||| || ||||| ||
--------gtaagcaccta-atataa--tgatgtttctttttctttattggctttattttttactaagattttaacctgttttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAG
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 13
-------------------gtgagtcaactcgtacttacatttaaactaaaac---ctggtttgatatgct----tgcctcatttccatgtaaaactctttacatttctctgcgcagGTGGCTTGGCAAGATCACTTTAGAGACTTACATTTCCCAGTTTCATATATGGCTAAG
| | | || | | | ||| | | | || ||| || || | | || ||| | || | || || | | |||||||||||||||||| ||||| ||||| |||||||||||||||||||| ||| ||||
gtacgtgttctttaccttaattattgaaattccatgttaattggttttggatcattttgtttttatttggtgataagtatctttttttttctgaatttcccccacttttgtat-cagGTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 13
-------------------------------gtgagtcaactcgtactta--catttaaactaaaacctggt--ttgatatgcttgcctcattt------ccatgtaaaactctttacatttctctgcgcagGTGGCTTGGCAAGATCACTTTAGAGACTTACATTTCCCAGTTTCATATATGGCTAAG
| || | | || | |||| | | |||| || ||| || || ||| | | || | | ||||| | | |||||||||||||||||| ||||| ||||| |||||||||||||||||||| ||| ||||
gtatgtgttctttaccctaattattgaaattctatgttgattggttttggattattttgttttttatttggtgactgctatctttttttcttttttttttcttttctgaattttccccatttttgtat-cagGTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------gtgagtcaactcgta--cttaca----tttaaact---aaaacctggtttgatatgcttg----cctcattt--ccatgtaaaactcttta-------catttctctgcgc----agGTGGCTTGGCAAGATCACTTTAGAGACTTACATTTCCCAGTTTCATATATGGCTAAG
| | | |||| || || ||| |||| | | |||| | |||| ||| || | || | | | ||| || || || || || || |||||||||||||||||||| |||||||| ||||| || || || || ||| | ||
gtaagttctctttgatctatatgatttaagttgaatcatttgactcataacctcacaaaaatttatagtttagaaacattgttttttatatttagagataatagttaacaactctgatttctctaactgtgccacacctttgtgcttctagTTGGCTTGGCAAGATCACTTTGGAGACTTATATTTCTCAATTCCACATCTGGTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttgatatgcttgcctcatttccatgtaaaactctttacatttctctgcgcagGTGGCTTGGCAAGATCACTTTAGAGACTTACATTTCCCAGTTTCATATATGGCTAAG
gtttgat putative branch site (score: 5)
ctctttacatttctct putative PPT
tttacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcaactcgtacttacatttaaactaaaacctggtttgatatgcttgcctcatttccatgtaaaactctttacatttctctgcgcagGTGGCTTGGCAAGATCACTTTAGAGACTTACATTTCCCAGTTTCATATATGGCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA