Sequence
atgc intronic sequence ATGC exonic sequencegtttgcttttatgttatgtcattcatgcaaatatataatatgtgaaaactgaaaacttgtattcctgcacattaattcatgttagattctttatataattcatgttcattgtagTCTGAAAAATGAACTTGCAGATGGGAAAGGTTGGAGAGAAGCTTGATATCGACTTTGTAGTTTCCACTGGAGACAACTTCTATGACAATGGACTAACTAG
Basic information
species | Glycine max |
transcript | GLYMA08G06090.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G06090.2 (Glycine max), 3'ss of exon 1
lower sequence: AC202435.3_FGT003 (Zea mays), 3'ss of exon 6
gtttgcttttatgttatgtcattcatgcaaatatataatatgtgaaaactgaaaacttgtattcctgcacatta-attcatgttagattctttatataattcatgttcattgtagTCTGAAA--AATGAACTTGCAGATGGGAAAGGTTGGAGAGAAGCTTGATATCGACTTTGTAGTTTCCACTGGAGACAACTTCTATGACAATGGACTAACTAG--------------------
| | ||||| | | || | || | ||| |||| ||| || || || | | | | || || ||| || ||||||||| ||| || |||||||| |||||||||||||| | ||||| || ||||||||||| | || || || | |
-------------------------------------acgcacgggcactgacctataatgttgaagttcagaatatttgacttaggatctaactaatatgtttggcctgggaaatttgcaatcaatttttatgtagATGGGAAGGGTCGGGGAGAAGCTCGATATCGACTTTGTTATATCCACCGGGGACAACTTCTACAAGAACGGCCTCAAGGGCGTGCACGACCAGGCATTTA
upper sequence: GLYMA08G06090.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G351232_T01 (Zea mays), 3'ss of exon 8
gtttgcttttatgttatgtcattcatgcaaatatataatatgtgaaaactgaaaacttgtattcctgcacatta-attcatgttagattctttatataattcatgttcattgtagTCTGAAA--AATGAACTTGCAGATGGGAAAGGTTGGAGAGAAGCTTGATATCGACTTTGTAGTTTCCACTGGAGACAACTTCTATGACAATGGACTAACTAG--------------------
| | ||||| | | || | || | ||| |||| ||| || || || | | | | || || ||| || ||||||||| ||| || |||||||| |||||||||||||| | ||||| || ||||||||||| | || || || | |
-------------------------------------acgcacgggcactgacctataatgttaaagttcagaatatttgacttaggatctaactaatatgtttggcctgagaaatttgcaatcaattcttatgtagATGGGAAGGGTCGGGGAGAAGCTCGATATCGACTTTGTTATATCCACCGGGGACAACTTCTACAAGAACGGCCTCAAGGGCGTGCGCGACCAGGCATTTA
upper sequence: GLYMA08G06090.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G152447_T01 (Zea mays), 3'ss of exon 1
gtttgcttttatgttatgtcattcatgcaaatatataatatgtgaaaactgaaaacttgtattcctgcacattaattcatgttagattctttatataattcatgttcattgtagTCTGAAA--AATGAACTTGCAGATGGGAAAGGTTGGAGAGAAGCTTGATATCGACTTTGTAGTTTCCACTGGAGACAACTTCTATGACAATGGACTAACTAG--------------------
| || | | | |||| || ||| | | | | | ||| |||| ||| || || || | | | | || || || || ||||||||| ||| || |||||||| |||||||||||||| | ||||| || ||||||||||| | || || || | |
--------------------------------agattttttttaaaaaaaacaatgttgaagttcagaatatttgac----ttaggatctaactaatatgtttggcctgagaaatttgcaatcgattcttatgtagATGGGAAGGGTCGGGGAGAAGCTCGATATCGACTTTGTTATATCCACCGGGGACAACTTCTACAAGAACGGCCTCAAGGGCGTGCGCGACCAGGCATTTGMapped 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|8669911|gb|BE191018.1|BE191018EST: GTGACTGGGGAAGAAGAGGCGCTTACAACCAATCACAAGTTTCTTTCCAG TCTGAAAAATGAACTTGCAGATGGGAAAGGTTGGAGAGAAGCTTGATATCG
genomic: GTGACTGGGGAAGAAGAGGCGCTTACAACCAATCACAAGTTTCTTTCCAGgtttgctttt ... ttcattgtagTCTGAAAAATGAACTTGCAGATGGGAAAGGTTGGAGAGAAGCTTGATATCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattcctgcacattaattcatgttagattctttatataattcatgttcattgtagTCTGAAAAATGAACTTGCAGATGGGAAAGGTTGGAGAGAAGCTTGATATCGACTTTGTAGTTTCCACTGGAGACAACTTCTATGACAATGGACTAACTAG
cattaat putative branch site (score: 3)
attaattcatgttaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcttttatgttatgtcattcatgcaaatatataatatgtgaaaactgaaaacttgtattcctgcacattaattcatgttagattctttatataattcatgttcattgtagTCTGAAAAATGAACTTGCAGATGGGAAAGGTTGGAGAGAAGCTTGATATCGACTTTGTAGTTTCCACTGGAGACAACTTCTATGACAATGGACTAACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA