RetrogeneDB ID: retro_ppat_14

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545099.1:246452..247154(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S210_37V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S194_18V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_14
ATGGCGACATACTCCGGCGTCACCCCCCGTCATCTGGCACCACTGGTTCATTTGCTGGGAATCGTCAGCATGGTGCTTAT
GGCACTGTGGACGAAGTGCTTCCGGGGCGGGTACGGCCTCTCCGGTTCCGGGGTATTCAATCTCCATCCCTTGATCATGT
TTGCTGGGTTCATCTTTTTGTCAAGCGAAGCTATCGTCACGTACAAAATCCTTAGTGGAGACAAGAAGCTCCAGAAGAGA
GTGCACATGATTGTCCAGGGTGTAGCCATCTTTCTCGCCGTCCTGGGGGTCACTTTCGCGTACAAGTTCCACCTTGATAT
CGGCATCCAAAATTTCTACAGCCTGCACTCCTGGCTCGGTCTTATCACCATCACGCTGTATCTATTCCAGTGGATCTTAG
GGTTCATGGCTTTCTGGCAACAAAGTGTAGCAAAGGTGAAACGCGCAGAGCTACTCCCGTGGCATGTTTTTCTGGGCCTG
GCGGCGTACGCTACGGCTCTTGCAACTGCAGAGCTCGGGCTACTTGAAAAGGTCACGTTTCTTGAGAAAAGCGAATCCCC
GCCGCTGAGAATTTGGTCTGGTGAGGCCATGCTTGTGAACATCATCGGGATTGTAATCTTCCTACTGGGTGCATTTGTTG
TCTTGACCAGTCTGATACCAAGATCTCGGAAGGACAAAGGATACCGTGACTTGCTAGAGTGA

Alignment

ORF - retro_ppat_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATYSGLTHKQTAPLVHILGIVSIVLVIIWTYHYRGGYGLSGGPVFNVHPLLMIAGFIFLSSQAIISYKT
          MATYSG.T....APLVH.LGIVS.VL...WT...RGGYGLSG..VFN.HPL.M.AGFIFLSS.AI..YK.
Retrocopy MATYSGVTPRHLAPLVHLLGIVSMVLMALWTKCFRGGYGLSGSGVFNLHPLIMFAGFIFLSSEAIVTYKI

Parental  VSGDRTYQKAVHMTLQGVALLLGIVGILAAYKFHSDLKIQNFYSLHSWFGIITILLYLLQWILGFVSFWT
          .SGD...QK.VHM..QGVA..L...G...AYKFH.D..IQNFYSLHSW.G.ITI.LYL.QWILGF..FW.
Retrocopy LSGDKKLQKRVHMIVQGVAIFLAVLGVTFAYKFHLDIGIQNFYSLHSWLGLITITLYLFQWILGFMAFWQ

Parental  QSLSSSTRAELLPWHIFLGLGAFVTALATAELGLLEKLTFLQKG-APFVGLWAREAMLVNSIGISVLLFG
          QS.....RAELLPWH.FLGL.A..TALATAELGLLEK.TFL.K...P....W..EAMLVN.IGI...L.G
Retrocopy QSVAKVKRAELLPWHVFLGLAAYATALATAELGLLEKVTFLEKSESPPLRIWSGEAMLVNIIGIVIFLLG

Parental  MVVVLTAVMPNPRRHEGYSPL
          ..VVLT...P..R...GY..L
Retrocopy AFVVLTSLIPRSRKDKGYRDL

Legend:

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

Expression

RNA-Seq

Physcomitrella patens was not studied using RNA-Seq expression data.

ChIP-Seq

Physcomitrella patens was not studied using ChIP-Seq data.

EST

Physcomitrella patens was not studied using EST data.

TSS

Physcomitrella patens was not studied using FANTOM5 data.

Lab

retro_ppat_14 was not experimentally validated.

Homology

Retrocopy orthology:

Physcomitrella patens 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.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA005956	1 retrocopy	retro_oind_56,
Zea mays	GRMZM2G034668	1 retrocopy	retro_zmay_23,
Leersia perrieri	LPERR04G16060	1 retrocopy	retro_lper_17,
Hordeum vulgare	MLOC_12641	1 retrocopy	retro_hvul_22,
Oryza brachyantha	OB02G32980	1 retrocopy	retro_obra_5,
Oryza barthii	OBART02G25610	1 retrocopy	retro_obar_22,
Oryza glumaepatula	OGLUM02G26140	1 retrocopy	retro_oglu_26,
Oryza nivara	ONIVA02G28050	1 retrocopy	retro_oniv_34,
Oryza punctata	OPUNC02G23460	1 retrocopy	retro_opun_42,
Oryza rufipogon	ORUFI02G27020	1 retrocopy	retro_oruf_43,
Oryza sativa japonica	OS04G0533500	1 retrocopy	retro_osat_39,
Physcomitrella patens	PP1S194_18V6	1 retrocopy	retro_ppat_14 ,
Sorghum bicolor	Sb06g023650	1 retrocopy	retro_sbic_21,
Setaria italica	Si010957m.g	1 retrocopy	retro_sita_34,