RetrogeneDB ID: retro_lper_22

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 3:29563256..29564111(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR03G35760
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR04G03430
• Aliases: None
• Description: None

Sequence

>retro_lper_22
ATGGCGGCAGTGGCAGTCAGCAGTAGTAACCCTCCTGCTCCTCCGCCTAAGGACTATCGCGATCCTCCTCCTGCGCCGCT
GGTGGACGTGGGGGAGCTGGGCAAGTGGTCCCTGTACCGCGCCGTCATCGCCGAGTTCACCGCCACGCTGCTCTTCGTGT
GCGTCACCGTGGCCACCGTCATCGGCCACAAGCGGCAGTCGGACTCGTGCGCCGGCGCGGGCGTGCTGGGCATTGCCTGG
GCATTCGGTGGCACCATCTTCGTGCTCGTCTACTGCACCGCCGGCATCTCCGGCGGCCACATCAACCCAGCCGTCACCTT
CGCCATGCTTCTCGCGCGCAGGGTCTCGCTGCCGCGGGCCGCGCTCTACGTCATCGCGCAGTGCGTCGGCGCCACGTGCG
GCGCGGGCCTCGCCAGGGCGCTGCACGGCGGAGGGCACTACGAGCGGCACGGCGGCGGCGCCAACGAGCTGGCGGCGGGG
TACTCGACGGTCGCGGGGGTCGGCGCGGAGATGGTGGGCACCTTCGTGCTGGTGTACACGGTGTTCTCGGCGACGGACCC
CAAGCGCAAGGCCCGTGACTCTCACGTGCCGGTGCTTGCGCCGCTGCCCATCGGGTTGGCGGTGCTCGCCGTGCACCTGG
CCACCATCCCCATCACCGGCACCGGCATCAACCCGGCGCGCAGCCTGGGGCCGGCCGTCGTCTACAACGCCGGCAGGGCG
TGGAGTGACCAGTGGATGTTCTGGGTGGGGCCCCTCGCCGGCGCGGCCGCCGCAATGCTGTACCACCAGTACATCCTCAG
GGGCGCTGCCGCCAAGGCCTTCGCCTCCTCCTACCTCGCCCATTTTGCCGCCTAG

Alignment

ORF - retro_lper_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.27 %
• Parental protein coverage: 95.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEEPEHARPKDYTDPPPAPLFDVGELRLWSFYRALIAEFIATLLFLYITVATVIGYKVQSSADQCGGVGI
          S..P....PKDY.DPPPAPL.DVGEL..WS.YRA.IAEF.ATLLF...TVATVIG.K.QS..D.C.G.G.
Retrocopy SSNPPAPPPKDYRDPPPAPLVDVGELGKWSLYRAVIAEFTATLLFVCVTVATVIGHKRQS--DSCAGAGV

Parental  LGIAWAFGGMIFILVYCTAGISGGHINPAVTFGLLLARKVSVIRAVMYIVAQCLGGIVGVGIVKGIMKH-
          LGIAWAFGG.IF.LVYCTAGISGGHINPAVTF..LLAR.VS..RA..Y..AQC.G...G.G.........
Retrocopy LGIAWAFGGTIFVLVYCTAGISGGHINPAVTFAMLLARRVSLPRAALYVIAQCVGATCGAGLARALHGGG

Parental  QYNANGGGANMVASGYSKGTALGAEIIGTFVLVYTVFSATDPKRNARDSHVPVLAPLPIGFAVFMVHLAT
          .Y...GGGAN..A.GYS.....GAE..GTFVLVYTVFSATDPKR.ARDSHVPVLAPLPIG.AV..VHLAT
Retrocopy HYERHGGGANELAAGYSTVAGVGAEMVGTFVLVYTVFSATDPKRKARDSHVPVLAPLPIGLAVLAVHLAT

Parental  IPITGTGINPARSIGAAVIYNQKKAWDDHWIFWAGPFIGALAAAAYHQYILRAAAIKALGS
          IPITGTGINPARS.G.AV.YN...AW.D.W.FW.GP..GA.AA..YHQYILR.AA.KA..S
Retrocopy IPITGTGINPARSLGPAVVYNAGRAWSDQWMFWVGPLAGAAAAMLYHQYILRGAAAKAFAS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Leersia perrieri was not studied using RNA-Seq expression data.

ChIP-Seq

Leersia perrieri was not studied using ChIP-Seq data.

EST

Leersia perrieri was not studied using EST data.

TSS

Leersia perrieri was not studied using FANTOM5 data.

Lab

retro_lper_22 was not experimentally validated.

Homology

Retrocopy orthology:

Leersia perrieri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009362	1 retrocopy	retro_oind_43,
Oryza longistaminata	KN540828.1_FG001	1 retrocopy	retro_olon_7,
Leersia perrieri	LPERR04G03430	1 retrocopy	retro_lper_22 ,
Oryza brachyantha	OB0038G10090	1 retrocopy	retro_obra_3,
Oryza barthii	OBART04G05050	1 retrocopy	retro_obar_18,
Oryza glumaepatula	OGLUM04G04240	1 retrocopy	retro_oglu_29,
Oryza meridionalis	OMERI04G05010	1 retrocopy	retro_omer_6,
Oryza nivara	ONIVA04G03300	1 retrocopy	retro_oniv_20,
Oryza punctata	OPUNC04G04310	1 retrocopy	retro_opun_34,
Oryza rufipogon	ORUFI04G05780	1 retrocopy	retro_oruf_16,
Oryza sativa japonica	OS04G0233400	1 retrocopy	retro_osat_19,