Sequence
atgc intronic sequence ATGC exonic sequence...tttgtaaatcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G67430.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 3'ss of exon 5
-----tttgtaaatcacttacattgatagctttttgtaatccattg----tatgactcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
||||| ||| ||| | |||| | | | | || | || |||| | | ||||||||||||||||| ||| |||||||||||| | || |||||||||||||||| || || || ||||||
gtaagtttgtcaatacctttttgtatgctctttgtagagttcggtgatgctttgtctcatgagcaaatgatactttgcagCTTACATGTCCTCCCCGTGCCACATTGAGCTTATCCTGTCAGAGAAGGAAGAACCAGTGAAGAAAGAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G702426_T01 (Zea mays), 3'ss of exon 5
tttgtaaatc-acttacattgatagctttttgtaat-ccattgtatgactcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
| | ||| | | | | || ||| | | ||| ||| | || | || || |||||||||||||||| ||| |||||||||||| ||||| |||||||||||||||||||||| || ||||||
-gtatgtatcgaaggatggtctttcattcttgcgacactgttgaatggtatatttaatgttgctgttctgcagCTTACATGTCCTCCCCTTGCCACATTGAGCTGATTCTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G148744_T02 (Zea mays), 3'ss of exon 5
---------tttgtaaatcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
| | ||| | |||| || || | | | || || | | || | || | |||||| ||||||||| || |||||||||||| |||| ||||||||||||||||||||||| || ||||||
gtacgtatcgtattgaatgatggccattcatta-ttgtaacagtgcagaatagtatatatttaattttgccgttctgcagCCTACATGTCCTCACCTTGCCACATTGAGCTGATCTTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G119169_T04 (Zea mays), 3'ss of exon 4
---------tttgtaaatca--cttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
| || | | | | | || || || | ||| | | | || | | | | |||||||||||||||| ||| |||||||| || | || |||||||||||||||||||| || || ||||||
gtaagtcagtctgaagttgaagttcgctatgctatgaacaggttactatttgca-gcttaagatcctacctacctggtgcagCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G119169_T01 (Zea mays), 3'ss of exon 6
---------tttgtaaatca--cttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
| || | | | | | || || || | ||| | | | || | | | | |||||||||||||||| ||| |||||||| || | || |||||||||||||||||||| || |
gtaagtcagtctgaagttgaagttcgctatgctatgaacagGTTACTATTTGCA-GCTTAAGATCCTACCTACCTGGTGCAGCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGA--------
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
-------------------tttgtaaatcacttacattgatagctttttgtaatccattgtatgac--tcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
||| | | || | || || | || | | || || ||||| || || | | |||||||||||||| |||||||||||| ||| | || ||||| ||||||||||| || || || ||||||
gtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttcttcatttggagcttaacattctgtttgcctacctgg--tccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G37160.1 (Glycine max), 3'ss of exon 5
-tttgtaaatcactt-----acattgatagctttttgtaat-ccattgtatgactcagtt-----tgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
| ||| | | | || | |||| ||| || | | | ||| ||| | ||| ||| || || |||||||||||||||| ||||||||||||||| |||| ||||| ||||||||||||||||| || ||||||
gtatgtcactgattttgttgatattgtcgacttaatggactactattacatgcttttgttgagagagtcctttttttttgcagCTTACATGTCATCTCCATGCCACATTGAGCTGATATTGTCTGAGAAGGAAGAGCCTGTGAAGAAAGAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G01110.1 (Glycine max), 3'ss of exon 5
-------------tttgtaa--atcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
||||| |||||| || || || | || | | | | | |||| | || ||||||| || |||||||||||||||| ||||||||||||||| |||| || || |||||||||||||| || || || |||
gtatgtcgctggttttgttgctatcactgac-ttaatggattactattacttact-tatg-ttgagagtgtctttttt--ttgcagCTTACATGTCATCTCCATGCCACATTGAGCTGATATTATCTGAGAAGGAAGAGCCGGTGAAGAAGGAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0010g03370.t01 (Vitis vinifera), 3'ss of exon 6
-------------tttgtaaatcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttg-cagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
|| |||| | | || | | | || ||| | | | | | | ||| ||| |||| || ||||| ||||||||| || |||||||||||||| || |||||||| ||||| ||||| |||
gtatgtttgtttcctttcaaatt--tatcttttgtgtatggtcgttttcctaaatgttgataggagccttctatttgtttggcagCATATATGTCATCCCCATGCCATATCGAGTTGATTTTGTCCGAAAAGGAAGAACCTGTTAAAAAGGAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0010g03380.t01 (Vitis vinifera), 3'ss of exon 4
-------------tttgtaaatcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttg-cagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
|| ||||| | | || | |||| ||| | | | | | | ||| ||| |||| || ||||| |||||||| ||||||||||||||||| || |||||||| ||||| ||||| |||
gtaagtttgtttcctttcaaatctagcatttgtgtaa-tggttgttttcctaaatgttaacaggaaccttctatttgtttggcagCATATATGTCATCACCATGCCATATTGAGTTGATTTTGTCTGAAAAGGAAGAACCTGTTAAAAAGGAG
upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S22_76V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------tttgtaaatcacttacattgatagctttttgta-atccattgta--tgactcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
|| | || || ||| | ||| | | | | || | || | | |||||||||||||||| || ||||||||||| |||||| | || |||||||| | ||| || |||||||||
gtaagtcgctcctttgtcccacttttgtattgtcgtttcttcagttctcgattctctaggacgatcgtgaaagacgtatctgtgaaacttatgctaattctttattttgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
agcttac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtaaatcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - taaatca
- - - - - -cttacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaccc