Sequence
atgc intronic sequence ATGC exonic sequencegtgcacatcttttctgtcaagatgacaaaatctttactagtgtagttgcataatcttagtgacaatattctgttcaactgcagGCTATACAGATGATTGACATCTATACCAGATTTGCTTATGAGCAAGCTGCAATACCTGTTGTTACAGGTCGAAAATCTAAAGTGGAAACATTTGCTGGTG
Basic information
species | Glycine max |
transcript | GLYMA09G24670.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 3'ss of exon 3
-------------------gtgcaca---tcttttctgt-caagatgaca-aaatctttactagtgtagttgcataatct--tagtgacaatattctgttcaactgcagGCTATACAGATGATTGACATCTATACCAGATTTGCTTATGAGCAAGCTGCAATACCTGTTGTTACAGGTCGAAAATCTAAAGTGGAAACATTTGCTGGTG
|||||| || || || | ||| ||| |||| | | || | |||| | || | | || || ||||| || || |||||||| | ||||| | |||||| || |||||||||||||| |||||| || | ||||||||||| | ||||||||| ||||||||||
gtttgttgaatgctaatcattgcacaagttccttcatgcacttgataacacaaattggaaagaatggaagattctaatgtaatatcatctgctccatttttctcttcagGCAATGCAAATGATTGATGTATATACAAAATTTGCATACGAGCAAGCTGCAATCCCTGTTATTCCGGGTCGAAAATCAAGAGTGGAAACGTTTGCTGGTG
upper sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------gtgcacatcttttctgtcaagatgacaaaatctttactagtgtagttgcataatcttagtgacaatattctgttcaactgcagGCTATACAGATGATTGACATCTATACCAGATTTGCTTATGAGCAAGCTGCAATACCTGTTGTTACAGGTCGAAAATCTAAAGTGGAAACATTTGCTGGTG
| | || ||||| | | | ||| || |||||| | | | | || || |||| | | || |||||||| || ||||||||||| | ||||||| |||||| | |||||| ||||||||||| ||| || ||||| ||||||| | ||| ||||||||||| ||||
gttagttttcacattttctttccaaattattgttgcttctgctgaaatttcaaagccatgcatgtgatggtgcaggaaagtcatttcttgataaacaatgaaagatt--ctagtgca-ctacctcatattctc--caat-tgttattgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCAATACCAGTTATTCCAGGTAGAAAATCAAGAGTAGAAACATTTGCGGGTG
upper sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 5
-------gtgcacatcttttctgtcaagatgacaaaatctttactagtgtagttgcataatcttagtgacaatattctgttcaactgcagGCTATACAGATGATTGACATCTATACCAGATTTGCTTATGAGCAAGCTGCAATACCTGTTGTTACAGGTCGAAAATCTAAAGTGGAAACATTTGCTGGTG
| | | | ||||| || | || ||| | ||| | | | | ||| | || ||| | ||||||| | ||||||||| || ||||| ||||||||||||| ||||||| ||||||| |||||| || ||||||||||||| || | || || ||||||||||
gtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgatta-gttttgt---attgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCAATTCCTGTTATTCCAGGTCGAAAATCAAAGTTAGAGACTTTTGCTGGTG
upper sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 5
gtgcacatcttttctgtcaagatgacaaaatctttactagtgtagttgcataatcttagtgacaatattctgttcaactgcagGCTATACAGATGATTGACATCTATACCAGATTTGCTTATGAGCAAGCTGCAATACCTGTTGTTACAGGTCGAAAATCTAAAGTGGAAACATTTGCTGGTG
|| ||| | ||| || | || | | | ||| | |||| | || | ||| |||||||||| ||||||||||||| ||||||| | ||||||||||||||||||||||||||||||| |||||||||||||||| |||||||| |||||||||||||
gtattcatgatatctatctgaaaaccactcctaatctttcttatgttttcttgtcttcatt-taacagattgta-aactgcagGCATTACAGATGATTGATGTCTATACAAAATTTGCTTATGAGCAAGCTGCAATACCTGTTATTACAGGTCGAAAATCAAAAGTGGAGACATTTGCTGGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatctttactagtgtagttgcataatcttagtgacaatattctgttcaactgcagGCTATACAGATGATTGACATCTATACCAGATTTGCTTATGAGCAAGCTGCAATACCTGTTGTTACAGGTCGAAAATCTAAAGTGGAAACATTTGCTGGTG
ttctgttc CT-rich tract
ataatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcacatcttttctgtcaagatgacaaaatctttactagtgtagttgcataatcttagtgacaatattctgttcaactgcagGCTATACAGATGATTGACATCTATACCAGATTTGCTTATGAGCAAGCTGCAATACCTGTTGTTACAGGTCGAAAATCTAAAGTGGAAACATTTGCTGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA