Sequence
atgc intronic sequence ATGC exonic sequence...attatgcgatttgagcttcatctacatgttcttgtgtctttagttatgtatctttgtgtttgttcttatattgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05330.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g10480.3 (Oryza sativa), 3'ss of exon 4
attatgcgatt-tgagcttcatctacatgttcttg--tgtctttagttatgta-tctttgtgtttgttcttatattgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
|| ||| ||||| | ||| | || | || |||||||| | | | || || | | ||| ||| | || | || || ||||||||| ||||| ||||||||||| ||| | || |||| |||||| ||||| || || ||||| || |||||||||
--cctgtcattatgagcataatcaggctattgtacactgattttagttaggggcttctcttgactgatagttccttg--caattaattgtttttttccttacagATCAGCTAATATAGGAGTATTCATATGCCTCAAGTGTTCCGGTGTTCACAGAAGTCTTGGCACACACATTTCAAAG
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G138349_T03 (Zea mays), 3'ss of exon 3
------attatgcgatttgagcttcatctacatgttcttgtgtctttagttatgtatctttgtgtttgttcttatattgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
|| | || | | ||| | | | | | |||| || | |||||| || | | ||||| || ||| | ||||||||| ||||| || |||||||||||| ||||||||| || || || || || ||||| || ||||||||||||
ttttctttttaacataaccaggtctgtatac-tatgcataggcctttgctt-caaacttttgtggctggagaaacac-aaataactgaggtttatctt---tgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G071582_T02 (Zea mays), 3'ss of exon 3
attatgcgatttgagcttcatctaca---tgttcttgtgtctttagttatgtatctttgtgtttgttcttatattgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
| | || | |||| | | | | || | | |||| | ||| | | ||| ||| | | | | | |||||| || || || ||||||||||||||| |||| |||| ||||| ||||| |||||||| || ||| ||||||||
cctttttaatcccaatgtcatgcatagtctatgctcaatcttacatcaatgtcccgttg-gctacttcactccttg--cgaataacaaactctgttcctgcagATCGGCTAACATTGGAGTATTCATTTGCCTAAAGTGTTCTGGTGTTCACAGAAGCCTCGGGACACATGTTTCAAAG
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------attatgcgatttgagcttca-----tctacatgtt-cttgtgtctttagttatgtatctttgtgtttgttcttatat--------tgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
|| || | |||| | | | | | || | | | || ||| | || || ||| | | || ||||| | | ||| || || ||||||| || || || || ||||| || || |||||||||||||||||||||||||| ||||| || |||||||| ||||||
gtaagtgtttaattttttcacgcatgactttgtggtttatattaattggcattatcatactatttttggtgtagtgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaaagaacatgtgaattaacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------attatgcgattt-----gagcttcatctacatgtt-cttgtgtctttagttatgtatctttgtgtttgttcttata-------ttgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
|| || | ||| || || | | || | | | || ||| | || || ||| | | || ||||| | ||| || || ||||||| || || || || ||||| || || |||||||||||||| ||||||||||| ||||| || |||||||| ||||||
gtaagtgtttaattttttcacacgtgacgttgtggtatatattaattggcattatcatacttttttcgatgaactgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaagaacgtgtgaattcacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 1
---attatgcgatttgagcttcatctacatgttcttgtgtctttagttatgtatctttgtgtttgttcttatattgaataatcagttagtagcttgttt--tcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
|| | | | |||| ||| || ||| | | || | | || | || |||||| ||| | || || || || |||| ||||| ||||| ||||| || | |||||||||||||| ||||||||||| || || ||| |||| || ||||||
taagttgtagggtaatagctacat--gaattttcctaaattgataatgtggaatgc--atattacttctta-gttgtgaatccatttttctaactgcttcttcagGTCAGCCAATATTGGAGTTTTTGTATGCTTAAAATGTTGTGGTGTGCACAGAAGTCTTGGCTCTCAAATATCAAAG
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 1
---attatgcgatttgagcttcatctacatgttcttgtgtctttagttatgtatctttgtgtttgttcttatattgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
|| | || ||| ||| || ||| | || | | || | | | | | | ||||| || | | ||||| ||||| ||||| ||||| ||| | ||||||||||| || ||||||||||| || || ||| |||| || ||||||
taagttgtaggaaactagcaacat--gaattttcctaaaatgataatgtggaatgcatat-tacctcttagttgtgaatccatttttctaactgcttcttcagGTCAGCCAATATTGGAGTTTTCGTATGCTTAAAATGCTGTGGTGTGCACAGAAGTCTTGGCTCTCAGATATCAAAG
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
----attatgcgatttgagcttcatctacatgttcttgtgtctttagttatgtatctttgtgtttgttcttatat-tgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
|| | | | | | || |||| |||| || | | ||| | || | | | ||||||| || || | | | ||||||| || |||||||| ||||| || || |||||||||||||| ||||||||||| ||||| || || ||||| ||||||
atttgacatccacacacaaatccgttta-atgtagctgtgaattca-tgttgttttcttcagcatatgcttatatatgtgtacttgaacaatg---cattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtatctttgtgtttgttcttatattgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
cttgttttc CT-rich tract
tttgttcttatattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attatgcgatttgagcttcatctacatgttcttgtgtctttagttatgtatctttgtgtttgttcttatattgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG
- - - -gatttga