Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaaacttccactacagcctctgtaccattgtcttaacgattgttattattctctttcgcaagttcagtatgaggatatgttcgactttgtgttttctttctgtttatgattcctctactattttttttgccagccaatcctcttctttaatcatctgtgttctgtgctgttatagGTATTAAATATGCTTTGCTGTTGGGTAGAAGACCCAAACTCAGAGGCTTTCAAGTTGCACCTACCAAGAATCCATGACTTTCTCTGGTTAGCTGAAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G07050.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G341010_T01 (Zea mays), 3'ss of exon 7
gtatgcaaacttccactacagcctctgtaccattgtcttaacgattgttattattctctttcgcaagttcagtatgaggatatgttcgactttgtgttttctttctgtttatgattcctctactattttttttgccagccaatcctcttctttaatcatctgtgttctgtgctgttata----gGTATTAAATATGCTTTGCTGTTGGGTAGAAGACCCAAACTCAGAGGCTTTCAAGTTGCACCTACCAAGAATCCATGACTTTCTCTGGTTAGCTGAAGATG
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-------------------------------------------------------------------------------aagtgtgtgccttagtgactagatta-gtataatattctta----actattcctataagcttgttccacaaattgctcccaaatatcaaataatattatacacagGTATTGAATATGCTTGCTTGTTGGATTGAAGACCCAAACTCAGAGGCATTCAAGCTCCATGTTCCTCGAATTTATGATTATTTGTGGCTTGCTGAAGATG
upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 8
gtatgcaaacttccactacagcctctgtaccattgtcttaacgattgttattattctctttcgcaagttcagtatgaggatatgttcgactttgtgttttctttctgtttatgattcctctactattttttttgccagccaatcctc-ttctttaatcatctgtgttctgtgctgttat--agGTATTAAATATGCTTTGCTGTTGGGTAGAAGACCCAAACTCAGAGGCTTTCAAGTTGCACCTACCAAGAATCCATGACTTTCTCTGGTTAGCTGAAGATG
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----------------------------------------------------------------------------------gcttcccttccatgttccccttatagattaattccacctaaaccagtaaatgcttaggaatactgattacctagttatgattctaatg-gttattattcagGTGTTAAATATGCTTTGCTGTTGGGTGGAAGATCCAAATTCTGAGGCCTTCAAGTTGCATCTTCCCAGGATTTATGATTATCTATGGATTGCAGAAGATG
upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 8
gtatgcaaacttccactacagcctctgtaccattgtcttaacgattgttattattctctttcgcaagttcagtatgaggatatgttcgactttgtgttttctttctgtttatgattcctctactattttttttgccagccaatcctcttctttaatcatc-tgtgttctgtgctgttatagGTATTAAATATGCTTTGCTGTTGGGTAGAAGACCCAAACTCAGAGGCTTTCAAGTTGCACCTACCAAGAATCCATGACTTTCTCTGGTTAGCTGAAGATG
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--------------------------------------------------------------------------------ttcttccctctttctgtttctatttgagaaattacagatgggctagctaaccctatcacctctttgctgctctaaactcaatgtatcctgtggcat-acagGTTTTAAATATGCTTTGCTGTTGGGTGGAAGATCCAAACTCAGAGGCTTTCAAGTTACATCTTCCTAGAATTTTTGATTTCCTGTGGCTTGCTGAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttgccagccaatcctcttctttaatcatctgtgttctgtgctgttatagGTATTAAATATGCTTTGCTGTTGGGTAGAAGACCCAAACTCAGAGGCTTTCAAGTTGCACCTACCAAGAATCCATGACTTTCTCTGGTTAGCTGAAGATG
ctttaat putative branch site (score: 4)
ttctttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaaacttccactacagcctctgtaccattgtcttaacgattgttattattctctttcgcaagttcagtatgaggatatgttcgactttgtgttttctttctgtttatgattcctctactattttttttgccagccaatcctcttctttaatcatctgtgttctgtgctgttatagGTATTAAATATGCTTTGCTGTTGGGTAGAAGACCCAAACTCAGAGGCTTTCAAGTTGCACCTACCAAGAATCCATGACTTTCTCTGGTTAGCTGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG