Sequence
atgc intronic sequence ATGC exonic sequencegtaagtattgcttcgatcctttgtggtgatgttaactatcttcttctactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ15373 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g38820.5 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------------------------------gtaagtattgcttcgatcctttgtggtgatgt----taactatcttctt------------ctactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
| | || || || | || |||| | ||| || || | || || || || || || || ||||| || |||||| | ||||| ||||| ||||| |||||||| ||||| ||| |||||||||||||||||| ||| | || ||
gtgagtcgtcgccctcgtcctcccccctcttgtgctctgctctgctctgctctgtcttcttttgagttttgagctttgagctcgttgtttgacttgtcgttggcggcgatgagatgtgactgggtttttgttgtggtggggcaacattacagGGCGAGCGATAAATGCCAGAGGGAGAAGCGCAAGACCATCAACGGCGACGACTTGCTGTGGGCGATGGCCACGCTGGGCTTCGAGGACTACATCGAGCCC
upper sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G064426_T02 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------------gtaagtattgcttcgatcctttgtggtgatgttaactatcttcttctac--tttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
|| || | || | || | || || || | ||| | |||| || || |||||||||||||| || |||||| ||||||| ||||||||||| ||| |||| ||||| ||| ||||||||| || ||||| || | |||||
gtaagtccctcggccgcggctgactctgactcttctgtttgcttggcatgttgggaattcagagtggcgtttcgcaaaccgcactttagcttaggtggggttttgtgttgacttgtctacgtccacgttccttgtctgctgtttgcagGGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCC
upper sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------gtaagtattgcttcgatcctttgtggtgatgttaa---ctatcttcttcta------ctttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
| || | ||| | | | ||| | ||| | | | || || | ||||| ||||| |||||||||||||| || |||||| ||||||| ||||||||||| || |||| ||||| ||| ||||||||| || || || ||| | |||||
gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
upper sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G05610.1 (Glycine max), 3'ss of exon 2
---------------------------gtaagtattgcttcgatcctttgtggtgat---gttaactatcttcttc--tactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
| | || | | || | | | || | || | | | | | || ||||| || || ||||| || ||||||||||||||||| ||||| ||||| || ||||| ||||| |||| ||| | || ||||||||||| | || ||
gtacacttctttgtttctcatgcgcgctttcattttttgtttgttattcgcgttaattgaatgaataaattgcgttgttgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGATTTGCTTTGGGCTATGACCACTTTAGGTTTCGAGGAGTATATTGATCCG
upper sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------------------------------------------------------------gtaagt-attgcttcgatcctttgtggtgatgttaactatcttcttctactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
| || || | | | || ||| || || || || | | || ||| || ||||| ||||||||||||||||| |||||||| |||||||| ||||| ||||| ||||| ||| ||| | || ||||| || ||| | || ||
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttgga-atattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC
upper sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT2G37060.3 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------gtaagtattgcttcgat----cctttgtggtgatgttaactatcttcttctactttg-----tagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
| || | |||| ||| | | | || ||||| | | |||| || ||| ||||| ||||| || || ||||||||||| |||||||| || ||||| ||||| ||||| ||||||||| || | || || || || ||| ||||||||
agtccttacattggttactctttcttgttgttcatctttgtttggctttgatgttgcatatttgatgatgcaatggtttttctatgacgttgatgagcagAGCGAGTGATAAATGTCAAAGAGAGAAAAGGAAGACTATTAATGGAGATGATTTGCTTTGGGCAATGGCTACTTTAGGATTTGAAGACTACATGGAACCT
upper sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv06s0004g03490.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------gtaagtattgcttcgatcctttgtggtgatgttaact-atcttcttcta--ctttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
| | || || | || | | | || | | | |||| |||| ||||| |||||||||||||| | |||||||||||||| || ||||| ||||| || ||||||||||| ||| | || || || || || | || |||
cttttgtttttccggtaaccaaacggggttagggtttttttttttttgttttttttgtttttaatttcaagataaattgactctgttctgggttttgaagAGCGAGTGACAAGTGCCAGAAGGAGAAGAGGAAGACAATTAATGGTGATGATTTATTATGGGCAATGGCTACGTTAGGGTTTGAAGATTATATTGATCCT
upper sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv08s0040g03260.t01 (Vitis vinifera), 3'ss of exon 1
------------------------gtaagtattgct--tcgatcctttgtggtgatgttaactatcttcttctactt----tgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
||| | | | | | || ||||| |||| | | || ||| | | ||| || ||||| || || || ||||||||||||||||| || ||||| ||||| ||||| ||||||||| || | || || ||||| || | || ||
gtatggctgatgcattttttctttttaattttaggcggtgcgtgattgatggtgttgttggttttgtttttcaattggatgcctagGGCGAGTGATAAATGTCAGAGAGAGAAGAGGAAGACTATTAATGGGGATGATTTGCTCTGGGCAATGGCGACTTTAGGGTTTGAGGATTATATTGATCCG
upper sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: EDP06643 (Chlamydomonas reinhardtii), 3'ss of exon 1
------------------------------------------------------------------------------------------------gtaagtattgcttcgatcctttgtggtgatgttaactatctt-------cttctactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
| | ||| | ||| | | ||| |||| | || ||| ||||| || |||||||||||||| | |||||| |||| || || || ||||| ||| |||| ||||| |||| ||| ||||||| ||||||||| |||| ||
gtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagtattgcttcgatcctttgtggtgatgttaactatcttcttctactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
tgttaac putative branch site (score: 2)
ctatcttcttctactt CT-rich tract
ttaactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtattgcttcgatcctttgtggtgatgttaactatcttcttctactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG