RetrogeneDB ID: retro_acar_69

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 1:130586325..130586880(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSACAG00000002653
• Aliases: None
• Description: Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:G1KB14]

Sequence

>retro_acar_69
AAAATTTATGGCTTCTATGATGAGTGCTTAAGGAAATAGGAAAACACTAACGTATGGAAATATTTCACAGACCTTTTTGA
CTATCTTCCTCTAACTGCCTTGGTGGATGGGCAGATTTTCTGTCTATATGGTGGCCTCTCTCGGTCTATAGTTACACTGG
ATCATATCAGAGCAATTGATTTCCTACAAGAAGTTGCACATGAGGATCCAATATGCGATTTGCTGTGGTCAGACCCTGAT
GATCATGGTGGTTGGGGCATCTCACCTCAAGGAGCTGGTTATACTTTTGAGCAAGATATTTCAGAAACTTTCAACCATGC
TAATGGCCTTACCTTGGTTTCAAGAGCTCATCAGTTGGTAATGGAGGGATACAATTGGTGCCATGATCGGAATGTAGTAA
CAATTTTCAGTGCTCCAAATTACTGTTACTGTTGTGGTAACCAAGGTGCAATCATGGAACTAGATGATATTCTGAAATAC
TCATTTTTGCAGTTTGATCCTGCACCACGCAGAGGTGAAGCACATGTCACTCATCGCACTCTAGACTACTTCCTA

Alignment

ORF - retro_acar_69 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.11 %
• Parental protein coverage: 59.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGP
          ..YGFYDECLRK..N.NVWKYFTDLFDYLPLTALVDGQIFCL.GGLS.SI.TLDHIRA.D.LQEV.HE.P
Retrocopy KIYGFYDECLRK*ENTNVWKYFTDLFDYLPLTALVDGQIFCLYGGLSRSIVTLDHIRAIDFLQEVAHEDP

Parental  MCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPN
          .CDLLWSDPDD.GGWGISP.GAGYTF.QDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPN
Retrocopy ICDLLWSDPDDHGGWGISPQGAGYTFEQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPN

Parental  YCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTRRTPDYFL
          YCY.CGNQ.AIMELDD.LKYSFLQFDPAPRRGE.HVT.RT.DYFL
Retrocopy YCYCCGNQGAIMELDDILKYSFLQFDPAPRRGEAHVTHRTLDYFL

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
SRP009831_adrenal	0.00 RPM	136.54 RPM
SRP009831_brain	0.00 RPM	154.23 RPM
SRP009831_dewlap	0.00 RPM	166.09 RPM
SRP009831_embryo	0.00 RPM	225.64 RPM
SRP009831_heart	0.00 RPM	60.03 RPM
SRP009831_liver	0.00 RPM	58.57 RPM
SRP009831_lung	0.00 RPM	68.81 RPM
SRP009831_ovary	0.00 RPM	197.37 RPM
SRP009831_skeletal_muscle	0.04 RPM	18.14 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_69 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_69 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis 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 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69 ,
Bos taurus	ENSBTAG00000000469	1 retrocopy	retro_btau_1754,
Callithrix jacchus	ENSCJAG00000013634	2 retrocopies	retro_cjac_1346, retro_cjac_4113,
Dasypus novemcinctus	ENSDNOG00000013011	4 retrocopies	retro_dnov_1025, retro_dnov_1844, retro_dnov_2100, retro_dnov_2122,
Echinops telfairi	ENSETEG00000007561	2 retrocopies	retro_etel_1233, retro_etel_659,
Felis catus	ENSFCAG00000029685	1 retrocopy	retro_fcat_1086,
Homo sapiens	ENSG00000113575	1 retrocopy	retro_hsap_369,
Mustela putorius furo	ENSMPUG00000010169	1 retrocopy	retro_mputfur_633,
Nomascus leucogenys	ENSNLEG00000026729	1 retrocopy	retro_nleu_2441,
Otolemur garnettii	ENSOGAG00000009695	2 retrocopies	retro_ogar_3414, retro_ogar_921,
Rattus norvegicus	ENSRNOG00000005389	5 retrocopies	retro_rnor_1263, retro_rnor_1264, retro_rnor_1265, retro_rnor_1266, retro_rnor_817,
Sorex araneus	ENSSARG00000005447	3 retrocopies	retro_sara_296, retro_sara_385, retro_sara_715,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Ictidomys tridecemlineatus	ENSSTOG00000010560	1 retrocopy	retro_itri_258,
Tursiops truncatus	ENSTTRG00000016859	1 retrocopy	retro_ttru_1584,