Sequence
atgc intronic sequence ATGC exonic sequencegtattttgattggattggtcatagagtttccagttcatttatatctaatttgggttcttagtttaatggttccttttatctgttagATAACATTCTTGAAGCAATTGCTAAATTGGGATTTACTGAGCCAACACCTATACAAGCTCAGGGATGGCCGATGGCGTTGAAGGGTAGGGATTTGATTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63120.2 |
intron # | 2 |
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 2
lower sequence: GRMZM2G362850_T01 (Zea mays), 3'ss of exon 3
--gtattttgattggattggtcatagagttt---ccagttcatttatatctaatt----tgggttcttagtttaatggttcct--tttatctgttagATAACATTCTTGAAGCAATTGCTAAATTGGGATTTACTGAGCCAACACCTATACAAGCTCAGGGATGGCCGATGGCGTTGAAGGGTAGGGATTTGATTGG
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gtttactctagttccagtgtttcctgtgcgtgtgtccgttgaaaataacgcaatacctgtgatttcttacactactgtttcatgactcttttgacagATTACTGCATGCAAGCTATTGCCAAATCTGGATTTGTGGAGCCAACACCTATTCAATCTCAAGGTTGGCCTATGGCTTTGAAGGGTAGGGACCTGATTGG
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G324146_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------gtattttgattggatt--ggtcatagagtttc-cagttcatttatatctaatttgggttcttagtttaatggttcct--tttatctgttagATAACATTCTTGAAGCAATTGCTAAATTGGGATTTACTGAGCCAACACCTATACAAGCTCAGGGATGGCCGATGGCGTTGAAGGGTAGGGATTTGATTGG
| | | || || | || |||| | ||| || | | || |||||| || | ||| || | | |||| || | |||| ||||| |||| ||||| |||| ||||||||||||| |||| || ||||| ||||| |||||||||||||| |||| |
gtttagtccacttccactgtttcctgtccgtgagtccgttgaaagtaatgcaatacctgtgagttcttatactactatttcacgattccttcgcaatacctatgatttcttatactaccgtttcacgattcctttaacagATTACTGCATGCAAGCGATTGCCAAATCTAGATTTGTGGAGCAAACACCTATACAATCTCAAGGTTGGCCTATGGCTTTGAAGGGTAGGGACCTGATATG
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC217043.3_FGT002 (Zea mays), 3'ss of exon 4
gtattttgattggattggtcatagagtttccagttcattta-tatctaatttgggttcttagtttaatggttccttttat--ctgttagATAACATTCTTG--AAGCAATTGC------TAAATTGGGATTTACTGAGCCAACACCTATACAAGCTCAGGGATGGCCGATGGCGTTGAAGGGTAGGGATTTGATTGG--------
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---cggccgtggaacaggaaagtgtccctgcagaacaggaactgttgaaaataacgcaatacct--gtgatttcttacactactgtttcatgactcttttgacagATTACTGCATGCAATCTATCTAGATTTGTGGAGCCAACACCTATTCAATCTCAAGGTTGGCCTATGACTTTGAAGGGTAGGGACCTGATTGATATCGCTC
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 2
gtattttgat-tggattggtcatagagtttccagttcatttatatctaatttgggttcttagtttaatggttccttttatctgttagATAACATTCTTGAAGCAATTGCTAAATTGGGATTTACTGAGCCAACACCTATACAAGCTCAGGGATGGCCGATGGCGTTGAAGGGTAGGGATTTGATTGG
|||||| | | |||| | | | ||| || | | | | | |||| | | || || | || || | ||||| | |||||||||||||| ||| ||||||||| ||||| || ||||| |||||||| ||||| || |||||||| ||||| |||||
gtatttcatcgttaaatggtgtcgcgctgtgaatctcaattttgt--acgtgtaacttttagctgattgagcttgttcacttgacagGGTATTGCCTTGAGGTGATTGCTAAATTGGGTTTTGTTGAGCCAACGCCTATTCAGGCTCAAGGATGGCCAATGGCCTTAAAGGGTAGAGATTTAATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttcatttatatctaatttgggttcttagtttaatggttccttttatctgttagATAACATTCTTGAAGCAATTGCTAAATTGGGATTTACTGAGCCAACACCTATACAAGCTCAGGGATGGCCGATGGCGTTGAAGGGTAGGGATTTGATTGG
ttccttttatctgtt CT-rich tract
atttatatctaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttgattggattggtcatagagtttccagttcatttatatctaatttgggttcttagtttaatggttccttttatctgttagATAACATTCTTGAAGCAATTGCTAAATTGGGATTTACTGAGCCAACACCTATACAAGCTCAGGGATGGCCGATGGCGTTGAAGGGTAGGGATTTGATTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG