RetrogeneDB ID: retro_acar_144

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 6:54097290..54098299(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB14
• Ensembl ID: ENSACAG00000012468
• Aliases: None
• Description: None

Sequence

>retro_acar_144
CCAAACCCAGCCACCAAGATGTTACTGGAAGCAATTATGAAGAATGGGAGTGCTGCCGGGAGTGGTGTGTACTGTCAAAC
ACCAGCAAATAGCAGTGATCAAAATAAACCTAATAATATAAAGGACAGCAGTGCAACTGCTGCACGTGAAAATGGGAAGA
CATATACCAAAGATCAAGTGGAAAGTATAAAGCAATGTAAAAAATCATTATGAAGTCCTTGAAGTTTCCAAAGATGCCAG
TGAAGAATACTTGAAGGAAGCTTATCAAAAACTTGCTCTGAAATTCCACCCAGACAAAAATTATCCACCAGGAGCAACAG
AAGCTTTAAAAAAAATGGAAATGCATATGGTGTGTTAAGCAATCAAGAAAAAAGAAAGCAGATTGACCACACAGGTGGTG
AAGAGCAATGCAGTCATCCTGGCAATGACAGATTTAACTTCCACAGGGACTGTGAAGCAGATATCACTTCAGAGGACCTT
GTCAATATGTTATTTGGAGGGGCATTTCCATCAGGTAGTGTGCATTCCTTTTCCAATGGATAGTCTGGAGACAGTCATCA
TTATCAGCAGTGCCACAGCGGACATGAAAGAGAAGAGAAGAGGGTTGATGGTGGCTTCTCTACGCTCGGTCAGCTAATGC
CAATTATTGTGCTAATCCTTGTATCTTTGCTGAAGCAGCTGATGGTGTCTTATCCTCCTTATTCCTTATATCGAGGATCG
GGTTCGGGGCAGACCACTGAGATGAAGACCAAAAACTTGGCACATTCCCGATTATGCCAACAAAGACTTTAAAAATGAAC
ACAAAGGTCCAAATTTTCAGAAGGTAGAAAAGAGTGTGGAAGAGGACTATGTGTCAAACATCCGAAATAACTGTTGGAAA
GAAAGACAGCAAAAAACAGATTTACTATGTGCAGCAAAAGTGTACTGAAATGAACAACTTCGAAGGAAAGCAGAAGCCAT
CTTTATAGATAACTGCAAAGAACTAGACAGATTGACCAGCCTCTATCAA

Alignment

ORF - retro_acar_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 89.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PTQAAKVLLEAIMKNGSAAGSGAYCRKPANSSDQSKPNNVKDSSATAAGESGKTYTKDQVEGVQSIKKCK
          P..A.K.LLEAIMKNGSAAGSG.YC..PANSSDQ.KPNN.KDSSATAA.E.GKTYTKDQVE...SIK.CK
Retrocopy PNPATKMLLEAIMKNGSAAGSGVYCQTPANSSDQNKPNNIKDSSATAARENGKTYTKDQVE---SIKQCK

Parental  -NYYEVLGVSKDAGEEDLKKAYRKLALKFHPDKNHAPGATEA-FKKIGNAYGVLSNPEKRKQYDLTGGEE
          .N.YEVL.VSKDA.EE.LK.AY.KLALKFHPDKN..PGATEA.FKK.GNAYGVLSN.EKRKQ.D.TGGEE
Retrocopy >NHYEVLEVSKDASEEYLKEAYQKLALKFHPDKNYPPGATEA<FKKNGNAYGVLSNQEKRKQIDHTGGEE

Parental  QCSHPGNGRFNFHRGCEADITPEDLFNMFFGGAFPTGSVHSFSNGRSGYSHHNQHRHSGHEREEERGDGG
          QCSHPGN.RFNFHR.CEADIT.EDL.NM.FGGAFP.GSVHSFSNG.SG.SHH.Q..HSGHEREE.R.DGG
Retrocopy QCSHPGNDRFNFHRDCEADITSEDLVNMLFGGAFPSGSVHSFSNG*SGDSHHYQQCHSGHEREEKRVDGG

Parental  FSMFIQLMPIIVLILVSLLSQLMVSNPPYSLYPRSGSGQTIEMKTENL-RIPYYVNKDFKNEYKGPNLQK
          FS...QLMPIIVLILVSLL.QLMVS.PPYSLY..SGSGQT.EMKT.NL..IP.Y.NKDFKNE.KGPN.QK
Retrocopy FSTLGQLMPIIVLILVSLLKQLMVSYPPYSLYRGSGSGQTTEMKTKNL>HIPDYANKDFKNEHKGPNFQK

Parental  IEKSVEEDYVSNIRNNCWKERQQKTDLLYAAKVYRDERLRRKAEAISMDNCKELERLTSLYR
          .EKSVEEDYVSNIRNNCWKERQQKTDLL.AAKVY..E.LRRKAEAI..DNCKEL.RLTSLY.
Retrocopy VEKSVEEDYVSNIRNNCWKERQQKTDLLCAAKVY*NEQLRRKAEAIFIDNCKELDRLTSLYQ

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	26.95 RPM
SRP009831_brain	0.00 RPM	51.41 RPM
SRP009831_dewlap	0.13 RPM	79.44 RPM
SRP009831_embryo	0.00 RPM	41.38 RPM
SRP009831_heart	0.00 RPM	33.41 RPM
SRP009831_liver	0.00 RPM	24.34 RPM
SRP009831_lung	0.00 RPM	44.28 RPM
SRP009831_ovary	0.08 RPM	88.30 RPM
SRP009831_skeletal_muscle	0.00 RPM	17.63 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_144 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_144 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.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012468	1 retrocopy	retro_acar_144 ,
Homo sapiens	ENSG00000164031	1 retrocopy	retro_hsap_1583,
Monodelphis domestica	ENSMODG00000020687	2 retrocopies	retro_mdom_1398, retro_mdom_752,
Nomascus leucogenys	ENSNLEG00000013668	2 retrocopies	retro_nleu_1761, retro_nleu_2409,
Otolemur garnettii	ENSOGAG00000005340	1 retrocopy	retro_ogar_120,
Pongo abelii	ENSPPYG00000014956	3 retrocopies	retro_pabe_1304, retro_pabe_982, retro_pabe_983,
Pan troglodytes	ENSPTRG00000016311	1 retrocopy	retro_ptro_1066,
Ictidomys tridecemlineatus	ENSSTOG00000021338	1 retrocopy	retro_itri_1840,