Sequence
atgc intronic sequence ATGC exonic sequence...agggcgtttagagtggctaggagttttttagggatcagtgttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtttgctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.5 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 9
----agggcgtttagagtggctaggagttttttagggatcagt--gttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtttgctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
| || | || | |||| | | | | | |||| | || | || | || || ||| | ||| | |||||||||||| |||||||||||||| || || ||| | ||| |||| || ||| ||||||| |||||||||||||| || ||||||||||||||| | ||
caatttgctcttcacagaaacccttttcttttcatgttttcattaacttcttccttttcaagttaatttagtgatacgggaaaaaac---ttgacttg---tgcagGGTTGTGATCGGATATGATGAAGGGACAATAATGATAAAAATTGGCCGTGAAGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAA
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 9
-agggcgtttagagtggctaggagttttttagggatcagtgttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtt-tgctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
|| | | | | | ||| | | | ||| || | || || ||| | | | | |||| | || | | | |||||||||||||||||||||||||| || || ||| | ||| |||| || ||| ||||||| ||||||||||| || || |||||||| |||||||| |||
aagaatttctctcattgaaacatgttgtgt-gagattttcattgacttgttctttc-ctgcataagtcaagttaatgatatggaatattttattttgtgtagGGTTGTGATTGGATATGATGAAGGGACAATAATGATAAAAATTGGTCGTGAAGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 9
agggcgtttagagtggctaggagttttttagggatcagtgttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtt-tgctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
| | | || | | | | | | || || || || ||| | | | || ||| || | | | ||||||||||||||||| |||||||| || || ||| | ||| |||| || ||| ||||||| ||||||||||| || || |||||||| |||||||| |||
taaagatatgttatcactgaaacatgtgtgagatttttaattggcttgttctttc-ctgcataagtcaagctaatggcatggaaaaacttattttgtgtagGGTTGTGATTGGATACGATGAAGGGACAATAATGATAAAAATTGGTCGTGAAGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 10
agggcgtttagagtggctaggagttttttagggatcagtgttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtttgctt-tacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
|| || | | || || | || || | | | | | |||| | | | ||||| || |||||||||||||| |||||||| || ||| |||| |||| || ||| ||||| ||||| ||||| || || || |||||||||||||| ||
----------------------gtattaaaaaaacttagtttcttgttttctccaattggtaa---gtgtttact-----tgaatatatcaattcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
-----------------------------------------------------agggcgtttag-agtggctaggagttttttagggatcagtgttagcaccttattaaactga-tcatacgggaccatcaacaacgaatgtgtttgcttta-cagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
| | | || | |||| || | | | | ||| |||| ||| | | || | || | | | | || | | ||||||||||||||| |||||||||||||| || ||||| |||||||| |||||| ||||||| ||||||||||||| ||||| ||||| || ||| |||||
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------agggcgtttagagtggctaggagtttt---ttagggatcagtgttagcaccttatta-----aactgatcatacgggaccatcaacaacgaatgtgtttgctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
| | |||||| | || | || | | | | | | || ||| |||| | | | || | || || || |||||||||||||||| |||||||||||||| || ||||| |||||||| |||||| | ||||| ||||||||||||| || || ||||| || ||| |||||
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaa---acagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 9
-agggcgtttagagtggctaggagtttttt-agggatcagtgttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtttgctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
| | | | | | | || || |||||||| ||| | || | | || |||| | | | || || |||| |||||||||||| || ||||||||||| || || ||||| |||||||| |||||| ||||| || |||||||| | || || ||||| || |||||||||
tgccgaatattatttactttttcttctcttgagaaatcagtgtctctctcttttcc--ctccttcttcgtgacctaaattaccaaaacctctttctttgcagGGTTGTGATAGGCTATGATGAAGGTACTATTATGGTCAAACTTGGCCGAGAAGAACCTGTAGCCAGCATGGATAACAGTGGGAAAATAATTTGGGCTAAG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
agggcgtttagagtggctaggagttttttagggatcagtgttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtttgctttaca----gGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
|| | || | || | ||| || ||| || | | | | | | || || | | ||||| | || ||||||| || || ||||||||||||| || ||||| |||||||| ||||| | ||||| || || ||||||| || |||||||| ||||||||||||
----tgtcacacttcacttctcttgttcctgtagccagcactaaatatttagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 9
agggcgtttagagtggctaggagttttttagggatcagtgttagcac-----cttattaaactgatcatacgggaccatcaacaacgaatgtgttt--------gctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
|| |||| || | || | ||||| ||| || | || | | || | ||| | | ||| ||||||||||||||||| || | ||||||||||||||| ||||| ||| |||| ||||| || || ||||| ||||| | ||| ||||| ||||||||||||||
-------------aaaatataggtttattttgaataattgttatcacactctctcaatatagttgctgtatgctttattcacatgtggcttctttttctttcctactttacagGGTTGTGATCGGTTTTGATGAAGGAACCATTATGGTGAAAATTGGTCGAGATGAACCAGTAGCTAGTATGGATAATAGTGGAAAGATCATATGGGCTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accttattaaactgatcatacgggaccatcaacaacgaatgtgtttgctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
aactgat putative branch site (score: 3)
tttgcttt putative PPT
attaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agggcgtttagagtggctaggagttttttagggatcagtgttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtttgctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA