RetrogeneDB ID: retro_rnor_1444

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:25865664..25866078(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000032666
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Trappc2l
• Ensembl ID: ENSRNOG00000014581
• Aliases: Trappc2l, RGD1304906
• Description: Trafficking protein particle complex subunit 2-like protein [Source:UniProtKB/Swiss-Prot;Acc:B2RYU6]

Sequence

>retro_rnor_1444
GCAGTGTGCATCGCGGTGATCGCCAAGGAGAATTACCCTCTGTACATCCGAAGCACTCCCACAGAGAACGAACTCAAGTT
CCACTACATGGTGCACACGTCTCTGGACGTGGTGGATGAGAAGATCTCTGCGAAGGGGAAAGCACTGGTGGACCAGAGAG
AGCTGTACCTGGGCCTGCTCTACCCAACCGAGGACTACAAGGTATACGGCTATGTGACCAATTCCAAGGTGAAATTTGTC
ATGGTGGTGGATTCCTCCAATACGGCCCTGCGGGACAATGAGATCCGCAGTATGTTCCGGAAGCTGCATAACTCCTACAC
AGATGTGATGTGCAACCCCTTCTACAACCCAGGAGACCGAATCCAGTCTAGGGCCTTTGATACCATGGTAACTTCGATGA
TGGCCCAGGTGTGC

Alignment

ORF - retro_rnor_1444 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.55 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVCIAVIAKENYPLYIRSTPTENELKFHYMVHTSLDVVDEKISAMGKALVDQRELYLGLLYPTEDYKVYG
          AVCIAVIAKENYPLYIRSTPTENELKFHYMVHTSLDVVDEKISA.GKALVDQRELYLGLLYPTEDYKVYG
Retrocopy AVCIAVIAKENYPLYIRSTPTENELKFHYMVHTSLDVVDEKISAKGKALVDQRELYLGLLYPTEDYKVYG

Parental  YVTNSKVKFVMVVDSSNTALRDNEIRSMFRKLHNSYTDVMCNPFYNPGDRIQSRAFDTMVTSMMVQVC
          YVTNSKVKFVMVVDSSNTALRDNEIRSMFRKLHNSYTDVMCNPFYNPGDRIQSRAFDTMVTSMM.QVC
Retrocopy YVTNSKVKFVMVVDSSNTALRDNEIRSMFRKLHNSYTDVMCNPFYNPGDRIQSRAFDTMVTSMMAQVC

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	15.89 RPM
SRP017611_kidney	0.00 RPM	12.14 RPM
SRP017611_liver	0.00 RPM	4.24 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1444 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1444 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1444 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000003547	1 retrocopy	retro_etel_1888,
Homo sapiens	ENSG00000167515	1 retrocopy	retro_hsap_4852,
Monodelphis domestica	ENSMODG00000003889	2 retrocopies	retro_mdom_1165, retro_mdom_1391,
Rattus norvegicus	ENSRNOG00000014581	3 retrocopies	retro_rnor_1444 , retro_rnor_1866, retro_rnor_2239,