Sequence
atgc intronic sequence ATGC exonic sequence...atatggaagacttaattatgctatgctacttttgttggaaaaaaaaagaaattcataaagcatatatactagtactcatcatttgaatttcaaaatgcagAAGAAGAAGATCCCCATGGCCCCAAATTTCCAACCAAGCACAACATCAGGATGGCAATGTATTGGCTTGCACAAGGATGTCAACCTGGAGACTCCCTGGT
Basic information
species | Glycine max |
transcript | GLYMA01G10880.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G10880.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G035928_T01 (Zea mays), 3'ss of exon 1
atatggaagacttaattatgctatgctacttttgttggaaaaaaaaagaa---attcataaagcatatatactagtactcatcatttgaatttcaaaatgcagAAGAAGAAGATCCCCATGGCCCCAAATTTCCAACCAAGCACAACATCAGGATGGCAATGTATTGGCTTGCACAAGGATGTCAACCTGGAGACTCCCTGGT---
|| | ||| ||| || || | | | ||| || | | || | || | || | | | || ||| | | ||| | |||| || || ||| | |||| | ||||| ||||| ||||| |||||||| ||||||||||||| ||||| |||||||||||||| || ||||
attttgaaactttatgtaccaagtgtaagtgcttttgataatgtggcgtttctactcttgaaccctagaaaattaaacacatttggttacattcttgcagAAGAACAAACGGACCCCTA------CAAAATCCCAACAAAGCATAACATAAGGATGGCCATGTATTGGCTTGTGCAAGGTTGTCAACCTGGAGATTCATTGGTGTT
upper sequence: GLYMA01G10880.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G155422_T01 (Zea mays), 3'ss of exon 1
atatggaagacttaattat--gctatgctacttttgttggaaaaaaaaaga---aattcataaagcatatatactagtactcatcatttgaatttcaaaatgcagAAGAAGAAGATCCCCATGGCCCCAAATTTCCAACCAAGCACAACATCAGGATGGCAATGTATTGGCTTGCACAAGGATGTCAACCTGGAGACTCCCTGGT---
| | ||| ||| || | | | |||| ||| || | | | | || | || | | |||| || ||| ||| |||||||||| || || | | |||| | ||||| ||||| ||||| ||||||| ||||||||||||| ||||| ||||||||||||||||| ||||
-ttttgaaacgttatgtactgagtgtagcaatttttttgataatgtgttgtttctacttttgaaccctaaaaa--agtaaacac--ttttaatacattcttgcagAAGAACAAA---CCGACCCCTACAAAATCCCAACAAAGCATAACATAGGGATGGCCATGTATTGGCTTGTGCAAGGTTGTCAACCTGGAGACTCATTGGTGTT
upper sequence: GLYMA01G10880.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0013g00220.t01 (Vitis vinifera), 3'ss of exon 1
atatggaagacttaattatgctatgctacttttgttggaaaaaaaaagaaattcataaagcatatatactagtactca----tcatttgaatttcaaaatgcagAAGAAGAAGATCCCCATGGCCCCAAATTTCCAACCAAGCACAACATCAGGATGGCAATGTATTGGCTTGCACAAGGATGTCAACCTGGAGACTCCCTGGT---
|||| | | | || | || | | | | ||||| | | | ||| | || | | || | |||| ||||||||||||| | || ||| |||||||| |||||||| || |||||||||| |||||| | |||||| |||||||| ||||||||||||||
---caatgaacttctgttagaattcctcatgaatttccattgtatatgtgtttcatcctgttcac-ttctaatgcttgattcttttctggaagtcaatttgcagAAGAAGAAATTG---ATCCTTACAAGAAGCCAACCAAACACAACATGAGAATGGCAATGTTTTGGCTAGTACAAGGGTGTCAACCAGGAGACTCCCTGGTGTT
upper sequence: GLYMA01G10880.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0013g00210.t01 (Vitis vinifera), 3'ss of exon 1
--atatggaagactt---aattatgctatgctacttttgttggaaaaaaaaagaaattcataaagcatatatactagtactcatcatttgaatttcaaaatgcagAAGAAGAAGATCCCCATGGCCCCAAATTTCCAACCAAGCACAACATCAGGATGGCAATGTATTGGCTTGCACAAGGATGTCAACCTGGAGACTCCCTGGT---
| || || | || |||||| || | ||| | | | || ||| | || | | || | | | ||| | | | | ||| ||||||||||||| || | || || ||||| | | ||||| || | |||| |||||||||||| |||||| |||||||||||||||||||| ||
ttagattgacaatttgataattatttcat-tcattttaactaaatatttcaaaaaaattatttataagattt--tgaaagtcaatttctaagt--caatttgcagAAGAAGAAAATGATCCTGATAGGAAG---CCAACTAGAGAGAACATGAGAAGGGCATTGTATTGGCTTGTACAAGGCTGTCAACCTGGAGACTCCCTAGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagaaattcataaagcatatatactagtactcatcatttgaatttcaaaatgcagAAGAAGAAGATCCCCATGGCCCCAAATTTCCAACCAAGCACAACATCAGGATGGCAATGTATTGGCTTGCACAAGGATGTCAACCTGGAGACTCCCTGGT
atttgaatttcaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatggaagacttaattatgctatgctacttttgttggaaaaaaaaagaaattcataaagcatatatactagtactcatcatttgaatttcaaaatgcagAAGAAGAAGATCCCCATGGCCCCAAATTTCCAACCAAGCACAACATCAGGATGGCAATGTATTGGCTTGCACAAGGATGTCAACCTGGAGACTCCCTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - -ttgttgg
- - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatata