Sequence
atgc intronic sequence ATGC exonic sequencegtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
Basic information
species | Glycine max |
transcript | GLYMA19G30100.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattg-gtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
|| || | || || | | || | ||| || |||| | | ||| | | | | | ||| | | | ||||| ||||| ||||||| || || |||||||||||||| ||||||||| | |||||||| |||||||| || ||||||||||| || ||||| || || || ||||
--------------------------------gtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcatta-ctctaattattttgctcgtaacttct--tcctgt-agATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
| || || ||||| | || | | || || || || ||| | ||| | | | || || ||| ||||||||||||||||| || |||||||| ||||||||||||||| | |||||||| |||||||| || ||||||||||| || ||||| || ||||| ||||
---------------------------------------------gtccttggatcatttctttcatagtctttgatgcaataaatttgc-ttgtattattaaattacattctta----ctggcagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAAATACAAA
upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
| || || || | || | || | | | | | || ||| | ||||| | || | | ||| |||||||||||||| || || |||||||| ||||||||||||||| | |||||||| |||||||| || || |||||||| || ||||| || ||||| ||||
---------------------------------------------gttcttggatcacttatttagttatagtcttcgatg-cagtaagt-ttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgt-cagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
||| | |||| | | || | | | | |||| ||| || |||| | ||| | ||| || | || | || || || |||||| || || ||| ||||| ||||| ||||||||||||||||||| ||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||||| || |||||||
gtatttttttagccctgtttg----gtcagatgacgcattcctgctctgttctcatgtgcccttatatatatgtaaaacattttat-----tatggtaatctaaggatttt--tggacactgaacagATTTTGAAAGAACTTCACAAATCTTGTCGAAGAGAAGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAA
upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
| | || || || |||| | || ||| || || || ||| ||| | ||| | | | | || | ||| | |||| |||||||| ||||||||||||||||||| ||||||||| |||||||| || ||||| || || || || |||| |||||||| || |||||||| |
-------------actccttggtatacatcag--tgttatgtagaataacttttatagttgca---ctgcatc-gtcagtagcatcatatgtgatgctgaccaatggtcgtgt-------gtttagATCTTGAAGGAGCTTCACAAATCTTGTCAAAAGGAAGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGA
upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------gtaacatattagtattttgtgcaatggtgtagg---ttgttttccagcttaatttgaatgtttctgtatc---tgta-tctattggtatccatgagcattgagtgatttattgat-tttgttgaaccctgt-----cagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
| | || || | ||| | | | || | | | |||| | | | | | |||| || |||| | | | | | | |||| | | |||| | | || ||||| |||||||| || || ||||||||||| | |||||||||||||||||| || ||||| || || ||| | ||||||| ||||| ||||| ||||| |
gtaagtattctgcccgttgactcctcaactttattttcatatctttcaactttatctagtattgaatgatttcgtttactcggaataccagtacttttcaaaatgggatgtaatgtgtagtaaattccttgttctgagaaaacttgtgatactcacagcttgtcgtacgtgcagATTTTGAAGGAGCTCCATAAATCTTGTCAGAAGGAAGATGGTACAGATGACCAGAAGAAGGGCACACAATTGCTGGAGGTGTATGCGATAGAGATTCAGA
upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------gtaacatat-tagtattttgtg-caatggtgtaggt---tgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
|| ||| | || | || || | | || | || ||| ||| | | | ||||| | | ||| | || ||| || | | || || | |||| | |||| ||||| |||||||| || |||||||||||||| | |||||||||||||||||||| ||||| || || ||| | | ||||||||||| ||||| ||||| |
gtaagttcgctgccagttgatttctccacaatatcttcatatgtcctattttatctgataataaatgtcagtcgcttatctcaatgcttttcagttcgagatatatgttcgcagaa-tatattttttcgta--cacaaatgtgagatgctt--ctaatttcttagaactg---cagATTTTGAAGGAGCTCCACAAATCTTGTCAGAAAGAAGATGGTACAGATGATCAGAAGAAGGGCACACAATTGCTCGAGGTTTATGCGATAGAGATTCAGAMapped 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|192319385|gb|FK009927.1|FK009927EST: AGCTTTGTAAGATCTTCTTTGATATTGGGGAATATGGGCGGATGAGTAAG ATATTGAAGGAACTTCACAAATCTTGTC
genomic: AGCTTTGTAAGATCTTCTTTGATATTGGGGAATATGGGCGGATGAGTAAGgtaacatatt ... accctgtcagATATTGAAGGAACTTCACAAATCTTGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
tattgat putative branch site (score: 3)
ccctgtc putative PPT
atttattgattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG