Sequence
atgc intronic sequence ATGC exonic sequence...tccattaaatgtatatatatgatcttagaaaattgtgtgagcttcttgatcagtgttacctacttgtttatgctggatttttgttgccaatcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
Basic information
species | Glycine max |
transcript | GLYMA17G34610.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g39260.1 (Oryza sativa), 3'ss of exon 6
tccattaaatgtatatatatgatcttagaaaattgt--gtgagcttcttgatcag--tgttacctacttgtttatgctggatttttgttgccaatcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
| || | || || | | || | ||| ||| | | | | |||| | || || | || ||||||| ||||| ||||||||| ||| | |||||||||||||| ||||||||||| ||||| ||||| |||||||| |||||| |||| | |||||| | |
------------------gtaattcttgagaacttttggtatcatgtttgtccagactaagatggaatgtcttatattt-atccttatacacatatggttacagGTCTTGAAGAGTGATGATGTGGATTTGATGATCATTGCCAGGGGAACACCTGGATTCTCAGGTGCAGACCTTGCTAACTTGGTTAATGTGGCTGCTCTTA
upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g39250.1 (Oryza sativa), 3'ss of exon 6
tccattaaatgtatatatatgatcttagaaaattgt--gtgagcttcttgatcag--tgttacctacttgtttatgctggatttttgttgccaatcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
| || | || || | | || | ||| ||| | | | | |||| | || || | || | ||||||| ||||| ||||||||| ||| | |||||||||||||| ||||||||||| ||||| ||||| |||||||| |||||| | || | |||||| | |
------------------gtaattcttgagaacttttggtatcatgtttgtccaggctaaaatggaatgtcttatagtt-atccttatacacatatgattacagGTCTTGAAGAGTGATGATGTGGATTTGATGATCATTGCCAGGGGAACACCTGGATTCTCAGGTGCAGACCTTGCTAACTTGGTAAATGTGGCTGCTCTTA
upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 6
tccattaaatgtatatatatgatcttagaaaattgtgtgagcttcttgatcagtgttacctacttgtttatgctggatttttgttgccaatcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
|||| | || || | | | | || | | | | | | |||| || | | | | | ||| | |||| | ||||||||| || ||||||||||||||||||||||||| || ||||| ||||| |||||||| |||||| | || ||||||| | |
------------------gtgattcttgagaactctt---gttcctgtgttattcaaatgaaatcgttttctcttaccgtcc--tatttgtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G463032_T01 (Zea mays), 3'ss of exon 5
tccattaaatgtatatatatgatcttagaaaattgtgtgagcttcttgatcagtgttacctacttgtttatgctggatttttgttgccaatcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
||||||| | || | | | || || | | || | | | | | | | | | | | ||| | |||| | ||||||||| || ||||||||||||| ||||||||||| || ||||||||||| |||||||| |||||| | || |||||||| | |
------------------gtgatcttgagaccttttattattttactgtcccac-tcgtatattgcctcttaccg------tcctactcgtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCTAGAGGAACACCGGGATTCTCTGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCTCTTA
upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G451483_T01 (Zea mays), 3'ss of exon 7
tccattaaatgtatatatatgatcttagaaaattgtgtgagcttcttgatcagtgttacctacttgttt---atgctggatttttgttgccaat-caagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
|| | | | | | || |||| |||||| || | || | |||||| | | ||||||||||| ||||| ||||||||||| || ||||| ||||| ||||| ||||| || ||||| |||||| | || | |||||| | |
------------------------------------gtaaatccttaaccttatatccatttctggtttggaatgctgacttggcaatcccttcatgatctcagGTTTTAAGAGCTGATGATGTGGATCTGATGATCATTGCAAGGGGAACTCCTGGTTTCTCAGGTGCAGATCTTGCGAACTTGGTGAATGTAGCTGCTCTGA
upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------------tccattaaatgtatatatatgatcttagaaaa---ttgtgtgagcttct-----------tgatcagtgttacctacttgtttatgc---tggatttttgttgccaatcaag----tacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
| | || | | |||| | || ||| || | ||| ||| |||| | | ||| || | | ||| | ||| | || | ||||||||||||||| |||||||||||||| ||||| ||||| |||||||| |||||||| || |||||||| |||||||||||| | || ||||||||| |||
gtattgtcaccctctaccaaaaattttaaggtgttttttgtacaatgaacactaagttggagtaaaaaagggctctacttttccagtcttgggaaggctttgcttgtgtgtctatttgcatggctgaccagtatcaaggttttgcttttccccttggcctaatgtatctaaatactattctacagGTTCTGAAGGGGGATGATGTTGATCTGATGATAATTGCTAGAGGAACTCCTGGGTTTTCAGGTGCTGATCTTGCAAACTTGGTCAATATTGCTGCTCTCAMapped 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|208117277|gb|GD918191.1|GD918191EST: ATCCGGATGTAAAAGGAAGACAGCAGATTTTGGAATCACACATGTCAAAG GTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCT
genomic: ATCCGGATGTAAAAGGAAGACAGCAGATTTTGGAATCACACATGTCAAAGgtatggtttt ... tcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCT
EST:
gi|8402478|gb|BE058112.1|BE058112EST: ATCCGGATGTAAAAGGAAGACAGCAGATTTTGGAATCACACATGTCAAAG GTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCT
genomic: ATCCGGATGTAAAAGGAAGACAGCAGATTTTGGAATCACACATGTCAAAGgtatggtttt ... tcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatcagtgttacctacttgtttatgctggatttttgttgccaatcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
tcttgat putative branch site (score: 4)
atttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccattaaatgtatatatatgatcttagaaaattgtgtgagcttcttgatcagtgttacctacttgtttatgctggatttttgttgccaatcaagtacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCAGAGGAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-ccattaa
- - - - - - - - - - - - - - - - -tgtgtga
- - - - - - - - - - - - - - - - - - - - gcttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgga