Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttttcatgtctttaatgcaagcgagagccttatctttggattctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA
Basic information
| species | Selaginella moellendorffii |
| transcript | EFJ11977 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os03g02380.2 (Oryza sativa), 3'ss of exon 4
--------------------------------------gtaagcttttcatgtctttaatgcaagcgagagccttatctttggattctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA
| | | | | || ||| | | ||| ||| | ||| | ||||||||| ||||| | || ||||| || || || | || |||||||| ||||| |||||||||||||||||||| || || ||||| || || || |
gtatgcttaactcatcttattggattgacagataaacagatatgtatcaaagttgacaatcggcattctgacatcatccttgaaatcttt--agATGAAAAAATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCAATGTATACTTTCGTCTTCCTCTGGACTCCGGCGTTGAGCCCAAATGAAGA
upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
----------------------------gta-agcttttcatgtctttaatgcaagcgagagccttat----ctttggattctatgt--agATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA
| | | | ||| | | | | | | ||||| | || | ||| || | ||||||||||||||| | || ||||| || || || | || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || || |
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
----------------------------gta-agcttttcatgtctttaatgcaagcgagagccttat----ctttggattctatgt--agATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA
| | | | ||| | | | | | | ||||| | || | ||| || | ||||||||||||||| | || ||||| || || || | || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || || |
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------------------------------------------gtaagcttttcatgtc-tttaatgcaagcgagagccttatctttggatt---ctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA
|| || | ||| | | || | | |||| | | || ||||| |||||||||||||||||| | || || |||||||| | ||||| || |||||||| || || || ||||||||||| || |||||||||||| | |||||
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA
upper sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------------gtaagcttttcatgtctttaatgcaagcgagagccttatctttggattctat----------gtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA
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gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|169055080|gb|FE461942.1|FE461942EST: CAAGACGCTTTTGACGCAGTTCAAAGTCGCCGGGTCTGCTATCGCCTCTG ATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCA
genomic: CAAGACGCTTTTGACGCAGTTCAAAGTCGCCGGGTCTGCTATCGCCTCTGgtaagctttt ... ttctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCA
EST:
gi|70671102|gb|DN839679.1|DN839679EST: CAAGACGCTNTTGACGCAGTTCAAAGTCGCCGGGTCTGCTATCGCCTCTG ATGAAAAGATTGCTCTCCTAGGAGCAAATCCA-TCTCTCTTCGAGGGGCTC
genomic: CAAGACGCTTTTGACGCAGTTCAAAGTCGCCGGGTCTGCTATCGCCTCTGgtaagctttt ... ttctatgtagATGAAAAGATTGCTCTCCTAGGAGCAA-TCCAATCTCTCTTCGAGGG-CTC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
32 (upstream exon),
25 (downstream exon)
Score:
4GCGGTTATCATGTTTACGTGGGCTGAGAACTACGGAGATCCTACCGAAAGCAAGACGCTTTTGACGCAGTTCAAAGTCGCCGGGTCTGCTATCGCCTCTGgtaagctttt ... ttctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagcttttcatgtctttaatgcaagcgagagccttatctttggattctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA
ctttaat putative branch site (score: 4)
tctttaat TA-rich tract
