Sequence
atgc intronic sequence ATGC exonic sequencegtattttattttttaatagtgtagttttcatgtctggttcttggatggaacatcaaagtttatgaatcatgattggcttgtcagGTGTTGAGATTGTAATTGCTACACCTGGTCGTTTGATTGATATGTTGGAATGTCAACACACTAATTTGAAGAGAGTGACTTACCTTGTACTGGATGAGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63120.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g68320.3 (Oryza sativa), 3'ss of exon 4
gtattttattttttaatagtgtagtttt--catgtctggttcttgg-atggaacatcaaagtttatgaatcatgattggcttgtcagGTGTTGAGATTGTAATTGCTACACCTGGTCGTTTGATTGATATGTTGGAATGTCAACACACTAATTTGAAGAGAGTGACTTACCTTGTACTGGATGAGGC
|| | || | || | | || | | || | || || | || || | | |||| ||||||||||| ||||| ||||||||||| ||||| |||||| ||||| || |||||||| || ||||| || ||||| || |||||||||||
------------gtatttgtcccatcttaccgaaaataattttggacataaggttttgtaggctaagtctcttgcgtctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAGGTGGTCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGC
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G02590.1 (Glycine max), 3'ss of exon 4
gtattttattt-tttaatagtgtagttttcatgtctggttcttggatggaacatcaaagtttatgaatcatgattgg--cttgtcagGTGTTGAGATTGTAATTGCTACACCTGGTCGTTTGATTGATATGTTGGAATGTCAACACACTAATTTGAAGAGAGTGACTTACCTTGTACTGGATGAGGC
||| | ||| || | ||| || | || | | || ||||| || | |||||| | |||| |||| |||| ||||| || || |||||||||||||||||| | || |||||||||||| ||| ||||| || |||||||||||||||||||||| ||||||| ||
gtacatggtttacttgcctattgcactttgataa-taattttggaat--aacatgaacatg-atgaataacttttggtgcttgccagGCGTTGAAATAGTTATTGCTACACCTGGTCGTCTAATAGATATGTTGGAAGCTCAGCACACAAACCTGAAGAGAGTGACTTACCTTGTCTTGGATGAAGC
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G09270.1 (Glycine max), 3'ss of exon 4
gtattttattttttaatagtgtagttttcatgtctggttcttggatggaacatcaaagtttatgaatcatgattg--gcttgtcagGTGTTGAGATTGTAATTGCTACACCTGGTCGTTTGATTGATATGTTGGAATGTCAACACACTAATTTGAAGAGAGTGACTTACCTTGTACTGGATGAGGC
||| | ||| | | | || | || ||||| | || || | |||| | | ||| ||||| |||| || || || || |||||||||||||||||| | || |||||||||||| ||| ||||| || || |||||||||||||||||| | ||||| ||
gtacatggtttacttgccttttgtactttgataataatttttggaataacca--gaacatgatgactaacttttgatgcttgacagGCGTCGAAATAGTTATTGCTACACCTGGTCGTCTAATAGATATGTTGGAAGCTCAGCACACGAACCTGCGGAGAGTGACTTACCTTGTCTTAGATGAAGC
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 4
gtattt-tattttttaatagtgtagttttcatgtc----tggttcttggatggaacatcaaagt-ttatgaatcatgattggcttgtcagGTGTTGAGATTGTAATTGCTACACCTGGTCGTTTGATTGATATGTTGGAATGTCAACACACTAATTTGAAGAGAGTGACTTACCTTGTACTGGATGAGGC
||| || | ||| || | || || | || | | | || ||| || ||| | |||| || || || ||||||||||||||| |||||||||||||| || || || |||||| |||| |||||| || || || |||||||||||||||||| | ||||||||
gtacttatgtttcttctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgccctta---tgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S59_81V6.1 (Physcomitrella patens), 3'ss of exon 5
---gtattttattttttaatagtgtagttttcatgtctggttct--tggatggaacatcaaagttta-----------tgaat--catgattggcttgt------cagGTGTTGAGATTGTAATTGCTACACCTGGTCGTTTGATTGATATGTTGGAATGTCAACACACTAATTTGAAGAGAGTGACTTACCTTGTACTGGATGAGGC
| | | | | |||| || | || ||||| | ||| || |||||| ||| | ||||| || ||| |||| |||||| |||| ||||| ||||| |||||||||||||| ||| ||||| ||| |||||| |||||| ||||||||| ||| | || |||| |||||
gttgggatgagctgtgtgcaagtggggtatgcagttctggggcggatgggtgatttgcggcagtttagggcgtgggcgtgagtaacatgaagtgcgtgtgtggtgcagGGGTTGAGGTTGTGATTGCAACACCGGGTCGTTTGATTGACATGCTGGAAGGTCGACACACGAATTTGCGGAGAGTGACGTACTTGGTGTTGGACGAGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtctggttcttggatggaacatcaaagtttatgaatcatgattggcttgtcagGTGTTGAGATTGTAATTGCTACACCTGGTCGTTTGATTGATATGTTGGAATGTCAACACACTAATTTGAAGAGAGTGACTTACCTTGTACTGGATGAGGC
aaagtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttattttttaatagtgtagttttcatgtctggttcttggatggaacatcaaagtttatgaatcatgattggcttgtcagGTGTTGAGATTGTAATTGCTACACCTGGTCGTTTGATTGATATGTTGGAATGTCAACACACTAATTTGAAGAGAGTGACTTACCTTGTACTGGATGAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA