Sequence
atgc intronic sequence ATGC exonic sequencegtattttttactttaaaaatatttggtttgttctactataaacagtataggtgttgtaaattcgttacaaatatacagaaaggataattgaaacttaattcagacagccaaccaaccatgtagGTCAGCTGTGTGCGCATGCTTTCTGGGGAGCGTGTGTTAACTGCATCCCATGATGGCACTGTGAAGATGTGGGATGTAAGAACAGATAGATGTGTTGCAA
Basic information
species | Glycine max |
transcript | GLYMA05G35210.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g39380.3 (Oryza sativa), 3'ss of exon 26
gtattttttactttaaaaatatttggtttgttctactataaacagtataggtgttgtaa-attcgttacaaatatacagaaaggataattgaaacttaattcagacagccaaccaaccatgtagGTCAGCTGTGTGCGCATGCTTTCTGGGGAGCGTGTGTTAACTGCATCCCATGATGGCACTGTGAAGATGTGGGATGTAAGAACAGATAGATGTGTTGCAA
| || || | | |||| ||||| || || ||| ||||| | | || ||| | | | |||| || | || || || |||| || | ||| || ||||| || || || ||||| | |||||||| |||||||||||||| ||||||||||||||| | || |||| |||||||| |
--------tgaaaatggggtagcgggatgttgctacaccaaacattac-----ttataacattcgcttccaaaatatccttatccagtcttacacttt-ttgacactgc----------tgcagGTTAGTTCTGTCCGGATGCTCTCAGGAGAACGTGTTCTTACTGCATCTCATGATGGCACTGTCAAGATGTGGGATGTACGTACCGATACTTGTGTTGCTA
upper sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 6
gtattttttactttaaaaatatttggtttgttctactataaacag-tataggtgttgtaaattcgttacaaatatacagaaaggataattgaaacttaattcagacagccaaccaaccatgtagGTCAGCTGTGTGCGCATGCTTTCTGGGGAGCGTGTGTTAACTGCATCCCATGATGGCACTGTGAAGATGTGGGATGTAAGAACAGATAGATGTGTTGCAA
| || || | || | ||| | |||| | |||| | | | || | || | | || || | | | ||||| || | ||| || ||||| || || || ||||| | | ||||||||||||||| |||||||||||||||||||| | || |||| ||||||| |
--------------------------gtgaggctcttacatttagctgtagat-ttgtttctatgttaacattgtctccttagtaactccaaagcatgttttgttcaat-----atcggtatagGTTAGTTCTGTCCGGATGCTCTCAGGAGAACGTGTCCTTATTGCATCCCATGATGGTACTGTGAAGATGTGGGATGTCCGGACTGATACTTGTGTTGTTA
upper sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 25
gtattttttactttaaaaatatttggtttgttctactataaacagtataggtgttgtaaattcgttacaaatatacagaaaggataattgaaacttaattcagacagccaaccaaccatgtagGTCAGCTGTGTGCGCATGCTTTCTGGGGAGCGTGTGTTAACTGCATCCCATGATGGCACTGTGAAGATGTGGGATGTAAGAACAGATAGATGTGTTGCAA
|| || |||| || | || | ||| | | | || | || || | | | | | ||| || | | | | ||| | | | | | | | || |||||||||||||||| ||||| || || || ||||| | ||||| |||||||||| |||||||||||||||||||| ||||| |||| ||||| ||||
-----------aatagaatcattt--ttgggtccaatatctagatt-taatcttggtgaa--aggttttattttttagagagt----tgaagaatcaatcc---ctgatatctatcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCATGATGGAACTGTGAAGATGTGGGATGTGAGAACTGATACGTGTGTGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatatacagaaaggataattgaaacttaattcagacagccaaccaaccatgtagGTCAGCTGTGTGCGCATGCTTTCTGGGGAGCGTGTGTTAACTGCATCCCATGATGGCACTGTGAAGATGTGGGATGTAAGAACAGATAGATGTGTTGCAA
acttaat putative branch site (score: 4)
ataattgaaacttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttttactttaaaaatatttggtttgttctactataaacagtataggtgttgtaaattcgttacaaatatacagaaaggataattgaaacttaattcagacagccaaccaaccatgtagGTCAGCTGTGTGCGCATGCTTTCTGGGGAGCGTGTGTTAACTGCATCCCATGATGGCACTGTGAAGATGTGGGATGTAAGAACAGATAGATGTGTTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC