Sequence
atgc intronic sequence ATGC exonic sequencegtaactctttcatgtttttagaactgttttggctggtggacaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
gtaactctttcatgtttttagaactgttttggctggtgg-acaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
|| ||| ||| | | || || | | || ||||||| | | | | | |||||| || | || | ||||||||||||| || ||||| ||||| ||||| || ||||| || | ||||||||| |||||||| ||||| ||||| || || ||||| | |||||||||
-------------gtagtta--actactcctgatgttgatatgtgcgaagcaattt-tgtccttaacgtggcgcacc-----ttaatatcgttcttt----acattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gtaactctttcatgtttttagaactgttttggctggtgg-acaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
|| ||| ||| | || || | | || ||||||| | | | | | |||||| || | || | ||||||||||||| || ||||| ||||| ||||| || ||||| || | ||||||||| |||||||| ||||| ||||| || || ||||| | |||||||||
-------------gtagtta--actacacctgatgttgatatgtgcgaagcaattt-tgtccttaacgtggcgcacc-----ttaatatcgttcttt----acattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 6
gtaactctttcatgtttttagaactgttttggctggtggacaa-gtgatgcaatttgtaaaggggatat-tgtctgctatcagctaatatttttt---tccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
| ||| || || |||| | |||| || ||| | | | | | | | || | | | || || || |||| ||||| || || || || ||||||||||| || |||||||||| |||||||||||||||||| ||||| ||||| || ||||| |||| || ||||||
-----------------------gtaatttctcttgttgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGGACTGGACAAATCAAAGAAGTTGAACGTGTAACCAGAGAGTCAAACTTCTATGAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
gtaactctttcatgtttttagaactgttttggctggtggacaa-gtgatgcaatttgtaaaggggatat-tgtctgctatcagctaatatttttt---tccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT----
| | ||| || | |||| | |||| || ||| | | | | | | | || | | | || || || |||| ||||| || || || || ||||||||||| || |||||||||| ||||||||||||||||| ||||| | ||| || ||||| |||| || ||||||
--------------------caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G102756_T01 (Zea mays), 3'ss of exon 4
gtaactctttcatgtttttagaactgttttggctggtggacaagtgatgcaatttgtaaaggggatat-tgtctgctatcagctaatatttttt---tccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
|| | | | |||| | | |||| || ||| | | | | | | || | | | || || || |||| ||||| || || || || ||||||||||| || ||||||||||| | ||||||||||||||| ||||| | ||| || ||||| |||| || ||||||
-------------------gtaatttctcttgctgacagcgga---atgcctttctcaaattatgcgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAAAATTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
---gtaactctt--tcatgtttttagaactgttttggctggtggacaagtg-atgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
|| |||||| || || | || | | | || | ||| || || ||||| | || | || || ||| | | |||| | | | | ||||||||||| || || || ||||| ||||| || ||||| |||| |||||||| |||||||| ||||||||||| || ||||| || | ||| ||||||
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaat--------tttctttatattc---atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaactctttcatgtttttagaa-ctgttttggctggtggacaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
| || | || || ||| | | | | || | || | ||| | | || | |||| || || ||| || ||| || || |||||||||||||| || || |||||||||||||| ||||| || |||||||| ||||| || |||||||||||||| |||||||| || | || ||||||
--------gtgatatagataaaatctgatctcgtttctgta-aacaagcacgattcttgtat------ttatatgcttatgtttacaatgtttctctctg----tgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaactctttcatgtttttagaactgttttggctggtggacaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
|||| | | ||| | | | |||| | ||| | ||||| || || | | | |||| | | || | | | | |||||| || || |||||||||||||| ||||||||||||||||| || ||||| || |||||||| ||||| || ||||||||||||||||||||||| || | |||||||||
gtaattttatcaagatcct---gctgtcattcctg-taaacaag-----caccatgca----gcaatttgtatttttatgacttacaatgtcttccctctg--tgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 20
gtaactctttcatgtttttagaactgttttggctggtggacaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
|||| | || | | ||| |||| | | | | | | || | | | || || | || |||| | | | ||| ||||||||||||||||||||||||||||||| ||||| || || || || ||||||||||| || |||||||||||||||||| ||||||||| || ||||||
gtaatttgtttag---taaggaagaactttgctttctttaggtgcggtacatcc---------aacttattttgtgattttcatatcgttttcttttggttcatggaacagTGAGGATCCTGACATTCACTTCAAGTATATTGAAGCTGCTGCTAAAACTGGACAAATTAAGGAGGTTGAGCGTGTGACTCGAGAATCAAACTTCTATGAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
-----------------------------gtaactctttcatgtttttagaactgttttgg---ctggtggacaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatattt------ttttccc--tgaact---------tgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
|| | ||| | ||||| || |||| ||||| || || | ||| || || || ||| || | | || | | || | |||| || | ||| ||||| ||||| || |||| ||||||||||||||| |||||||||||||| |||||||| || || || ||||| || ||||| || | || ||| |
gtgggaatttatgtcttttctttctttctgtt-tttttttttaattttaattttggcttggaatctggtatacg-gtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
agctaat putative branch site (score: 3)
agctaatattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactctttcatgtttttagaactgttttggctggtggacaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG