Sequence
atgc intronic sequence ATGC exonic sequencegtaaagctatagccactgcgatattggttggagttagtttggaaagagttttgtatataacttgtgtagttttggttgttcacagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTGGTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G15110.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G095757_T01 (Zea mays), 3'ss of exon 11
-----------gtaaagctatagccactgcgat-attggttggagttagt--ttggaaagagttttgtatataacttgtgtagttt--tggttgttcacagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTGGTAG
|| || |||| | | ||| | | |||| ||||| || | | | || | | || | | |||| | ||| | ||| ||||| | |||||||||||| | ||||| ||||| || |||| |||||||| ||||| || || ||||||||||||||||| ||
ggaatcaacgagttaatttata-ctagtgcaaccaagtgttgccattagtaattatgacaaatcttttctgaaataatttttgtttgataattgctttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTAGAGCTCCTGATCTGCATCAAGTTTGGGCATG----
upper sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 10
--------gtaaagctatagccact--gcgatattggttggagttagtttggaaagagttt---tgtatataacttgtgtagttt--tggttgttcacagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTGGTAG
| | ||| || || | | | | | | ||| | ||| | ||| | | | || | |||| | ||| | ||| ||||| | |||||||||||| | ||||| ||||| || |||| |||||||| || || || || |||||||||||||||||| |
caagttagtttatactagtgcaaccaagtgttgccattagtaattattatggcatttttttttctttctggaataataattgtttgacgattggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG----
upper sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------gtaaa-gctatagccactgc----gatattggttggagttagtttggaaagagtt------ttgtatataacttgtgtagttttg-gttgttca-cagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTGGTAG
| ||| |||| | | || | ||||| || | | |||| || || | ||| | | ||| || |||| ||||||||| ||||||||||||||||| || |||||||| || || | || ||||| | ||||| ||||| ||||||||||||||| ||
gtactatctctccttgcttatttgcaaatattatacttgatactaagaatgccaaccagcattagtgtgcatatagttcaaatttttcttacattttggtaaatgttgtgtcgttcttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagttagtttggaaagagttttgtatataacttgtgtagttttggttgttcacagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTGGTAG
atataac putative branch site (score: 3)
ttttgtatataactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagctatagccactgcgatattggttggagttagtttggaaagagttttgtatataacttgtgtagttttggttgttcacagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTGGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG