Sequence
atgc intronic sequence ATGC exonic sequencegttctctgtgaaaaagagagaggagattttcctacgacttggttctaaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
Basic information
| species | Selaginella moellendorffii |
| transcript | EFJ16044 |
| intron # | 8 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
----------------------gttctctgtgaaa--aagagagaggagattttcctac--gacttggttctaaaacttgtcattctttgttttc-acagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| ||| || || | | | ||| ||| | || | || | | || | | | |||| |||||||||||||||||||| ||||| ||||||||||| ||||| |||||||| || || || || | |||||||| || | || || || || |||||||
ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgtacattatccaatttgaaataaatcaatattgtgccctcatcccttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 13
-------------gttctctgtgaaaaagagagag---------gagattttcctac--gacttggttctaaaacttgtcattctttgttttc---acagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| | |||| | | | || | |||||| | | | || | | | ||| || ||||| || |||||||||||||||||||| || || || || |||||||| |||||||| ||||| ||||| ||||| | | || |||| || || || |
ttaaaaagtatttctgccctgtagagtactgccagttttcccctggcattttctaattgaaagtatgcataggattaattggacttgacatttgctgcagACATTTAATGGCAAGAAATGGGAGAAATTCAATAGTGAAAAGGTGGCGTCGCTCGCATACGCCCGGATTCAAGGAAGGAGTGCTTTGATTGCTCATTTTC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
-----------------------gttctctgtgaaaaagagagaggagattt--tcctac----gacttggttct---aaaacttgtcattctttgtttt----cacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| | ||| | ||| || | | || | | || || |||| | | || | | || | | | ||||| ||||| |||||||||||||||||||| || || ||||| |||||||| || |||||||| | ||||| || | | ||| |||| || || ||||
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
--------------------------------------------------------------------------------------gttctctgtgaaaaagagagaggagattttccta-cgacttg--gttctaaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| | | | | | | | || | |||| || | || | | | | | | | ||| ||||| || ||||| || || ||||||||||||||||| |||||||||||||| || || || || | |||||||| || | || ||||| || || ||||
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatcttttt---cagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G004455_T01 (Zea mays), 3'ss of exon 11
---------------gttctctgtgaaaaagagagaggagatt---ttcctacgacttggttctaaaacttgtc---------attctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| ||| | | ||| || || || || || || | || | | | | ||| | || ||||| ||||||||||||||||| ||||| |||||||| ||||| | || || || | || ||||| | | || ||||| | || || |
taataccgggagggcggtctttccctccccggccgagttttttttgtttctgtgaagaacttgaaagatttatttacagatgtacacctataacctgcagGCTTTTAATGGTAAGAAATGGGAGAAGTTCAACAGTGAGAAGGTAGCATCTTTGGCTTATGCTAGAATTCAAGGACGGTCTGCACTGATATCACATTTTC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------------------------gttctctg-tgaaaaagagagaggagattttcctacgacttggttctaaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
|| || | | ||| | | | | | | | | || | || | ||| | ||||| |||| || ||||| || || ||||||||||||||||| |||||||||||||| || || || || | |||||||| || | || ||||| || || ||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgcta--tcctgagctattttttcatcgttttt-cagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G154229_T01 (Zea mays), 3'ss of exon 11
-----------------------------------------------------------------------------------gttctctgtgaaaaagagagaggagatt-ttcctacgacttggttctaaaacttgt----cattctttgttttca-----cagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| | | | || | || || || || | || ||| | || | | | | | | ||| | || ||||| ||||||||||| ||||| |||||||||||||| || ||| | || || || | || ||||| | | || ||||| | || || |
gtgctttcctttcttggcctttgtcctgtgtttgcaatagttacctgcagagttaagaacttgttccctgtccagctgagttaatcagcaatacggattagcaatagtataattactctgaacagcttgtaatatttatgtactgatgtacatctataacctgcagGCTTTTAATGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTAGCCTCGTTGGCTTATGCTAGAATTCAAGGACGGTCTGCACTGATATCACATTTTC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
----------------------------------------------gttctctgtgaaaaagagagaggagattttcctacg-acttggttctaa------aacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| | | | | ||| | | || || |||| ||||| | || | || | | ||| ||||||||| |||||||||||||| || ||||| ||||| |||||||| || || || || || || ||||| || || || || || || |||||||
gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgatgcatt--tctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
-----------------------gttc--tctgtgaaaaagagagaggag-attttcctacgacttggttctaaaacttgtcattctttgttt-------tcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| || | |||| | | || | | || | | | ||| | | | || |||| | |||| | ||||| || ||||||||||| ||||| ||||||||||||||||||||||| || || | ||||| || || || | || || || || || ||||
gtataagctttgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
---------------gttctctgtgaaaaagagagaggagattttcctacgacttggttctaaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| | | | | | | |||| | | | | ||| || | | || ||||| | || |||||||| || ||||| ||||| || ||||||||||||||| |||| |||| || || |||||||| || | || || || || || ||||
gtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacatt--cacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 14
------------------gttctctgtgaaaaagagagag------gagat-tttcctacgacttggttct--aaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
|| | ||| | | |||| ||| | | || || | | || |||| | | | |||| ||| | |||||||| ||||||||||||||||| || ||||| ||||||||||| || || || || || || || || ||||| || || || || || ||||
aaataccacctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaattttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
-------------------------------------------------------------gttctctgtgaa-aaagagagaggagattttcctacgacttggttctaaaacttgtcat---------tctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| | ||| | | | | || | | | || ||| | |||| | || || | |||||||| | |||||||| || || ||||||||||| ||||| |||||||||||||| || || || || || || ||||| || | || || || || || ||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
upper sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------gttctctgtgaa-aaagagagaggagattttcctacgacttggttctaaaacttgtcat---------tctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
| | ||| | | | | || | | | || ||| | |||| | || || | |||||||| | |||||||| || || ||||||||||| || || |||||||||||||| || || || || | || |||| || | || || | || || ||||
gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaatttcataaggtctacaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCCMapped 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|169029427|gb|FE436695.1|FE436695EST: ACGCATTCATCAATATGCTGTCGCCTTCCTTGATCGTGTCCTTCTACCAG ACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCG
genomic: ACGCATTTATCAATATGCTGTCGCCTTCCTTGATCGTGTCCTTCTACCAGgttctctgtg ... gttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCG
EST:
gi|169051393|gb|FE457678.1|FE457678EST: ACGCATTCATCAATATGCTGTCGCCTTCCTTGATCGTGTCCTTCTACCAG ACGTTCAATGG
genomic: ACGCATTTATCAATATGCTGTCGCCTTCCTTGATCGTGTCCTTCTACCAGgttctctgtg ... gttttcacagACGTTCAATGG
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),
35 (downstream exon)
Score:
21AATAAGTGTAACGTCGGATACGCATTTATCAATATGCTGTCGCCTTCCTTGATCGTGTCCTTCTACCAGgttctctgtg ... gttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaggagattttcctacgacttggttctaaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
ttctaaa putative branch site (score: 21)
tcattctttgttttc putative PPT
ttctaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctctgtgaaaaagagagaggagattttcctacgacttggttctaaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
