Sequence
atgc intronic sequence ATGC exonic sequence...tgagttgcacacatttttgtgtattccgaaactgggattcgtcgttctctatatattggtaaaagcctgacgagacatcggatgaatcggtgttgcacagGTCCATATCAAGAAGGGACCTGGAAAATCCGAGTTGAATTGCCCGATGCTTATCCCTACAAATCTCCTTCCATTGGGTTTGTGAACAGGATCTTCCATCC
Basic information
species | Physcomitrella patens |
transcript | PP1S161_122V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S161_122V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G39370.1 (Glycine max), 3'ss of exon 1
----tgagttgcacacatttttgtgtattccgaaactgggattcgtcgttctctatatattggtaaaagcctgacgagacatcggatgaatcggtgttgcacagGTCCATATCAAGAAGGGACCTGGAAAATCCGAGTTGAATTGCCCGATGCTTATCCCTACAAATCTCCTTCCATTGGGTTTGTGAACAGGATCTTCCATCC
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ttgttgttttgtcc-tgttttgagatctttatcaatatttctgtattatgcaccttcctttttcaatagtctttttt--tatctgtttgatggcttttg-gcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
upper sequence: PP1S161_122V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G46940.1 (Glycine max), 3'ss of exon 2
tgagttgcacacatttt-tgtgtattccgaaactgggattcgtcgttctctatatattggtaaaagcctgacgagacatcggatgaatc--ggtgttgcacagGTCCATATCAAGAAGGGACCTGGAAAATCCGAGTTGAATTGCCCGATGCTTATCCCTACAAATCTCCTTCCATTGGGTTTGTGAACAGGATCTTCCATCC-
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----ttgtcctgttttgatatccttttcaatatttctgtatcatgtaccttcctttttcaatagtatttttttatccgtttgatggcttttggcttttggcaggTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGCTTTATCAACAAGATCTATCACCCA
upper sequence: PP1S161_122V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv17s0000g07960.t01 (Vitis vinifera), 3'ss of exon 4
tgagttgcacacatttttgtgtattccgaaactgggattcgtcgttctctat-atattggtaaaagcctgacgagacatcg-gatgaatcggtgttg--cacagGTCCATATCAAGAAGGGACCTGGAAAATCCGAGTTGAATTGCCCGATGCTTATCCCTACAAATCTCCTTCCATTGGGTTTGTGAACAGGATCTTCCATCC
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----ctatgacagcacttttcttttcagaaaggccacttggctgtttaaggttatattcttttgtatttgatatttaactgtgatctggctgtgatggctgcagGCCTCTATGAGGGTGGGGTGTGGAAAATTCGTGTTGAACTCCCAGATGCTTATCCTTACAAGTCTCCTTCTATTGGGTTTGTCAACAAGATTTTCCATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctatatattggtaaaagcctgacgagacatcggatgaatcggtgttgcacagGTCCATATCAAGAAGGGACCTGGAAAATCCGAGTTGAATTGCCCGATGCTTATCCCTACAAATCTCCTTCCATTGGGTTTGTGAACAGGATCTTCCATCC
gcctgac putative branch site (score: 3)
atatattggtaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgagttgcacacatttttgtgtattccgaaactgggattcgtcgttctctatatattggtaaaagcctgacgagacatcggatgaatcggtgttgcacagGTCCATATCAAGAAGGGACCTGGAAAATCCGAGTTGAATTGCCCGATGCTTATCCCTACAAATCTCCTTCCATTGGGTTTGTGAACAGGATCTTCCATCC
- - ttgcaca