RetrogeneDB ID: retro_acar_16

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 1:181137094..181138222(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000001690
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000009588
• Aliases: None
• Description: None

Sequence

>retro_acar_16
CGTCGTCCGCTGCTTTCGCGTCCCTGCAACCGGCCTTCGGTCGCCAAGGACAGGGTATTGTGTTTCTCTGTCAGCATCAC
CATGCTTCACCATGACCGCCAAGTTCATTACTCTGTAATTCCCCATGGAAAAAGTGGGCGCTCTTCCGTCAGTGGCGTAG
TGGCTACTGTCTTTGGGGCCACAGGATTCCTGGGTCGATATGTTGTTAACCGCCTGGGGCGCATTGGTTCCCAAGTCGTC
ATCCCATATCGCTGTGATCAGTATGACCTCATGTACCTTCGACCCATGGGTGACCTAGGACAGCTTCTTTTTATGGAATG
GGATTCTCATGACAAAGATTCTATCCGAAGAGCTCTTGAATACAGTAATGTTGTTATCAATCTTATTGGAAAAGAATGGG
AAACAAGAAGCTTCAAGTATGAAGATGTCTTTGTTAATATTCCCAGAAATATTGCCCAGCTCTCAAGGGAAGTTGGAGTA
GAAAAATTAATTCACATTTCCCACCTGAATGCAGATGTGAAAAGTCCTTCAAAATACCTTAGGAATAAAGCTATTGGAGA
GAGAGTCGTAAGGGAAGAATTTCCAGATGCTATCATTTTGAAACCTTCTGAAATGTTTGGGAGAGAAGATAGGTTTTTCA
ATCATTATGCAAATATGCATTGGTTTGGTGGAGTTCCACTGATTGCATTTGGAAGAAAAACTGTAAAACAGCCTATCTAT
GTTTCTGATGTTGCCAAAGCAATCATTAGTGCTATTAAGGATCCTGATGCAAAAGGAAAAACATACACATTGACTGGCCC
TCACAGATACCTCCTTTATGACTTGGTACAGTATCTATATGCAGTGCTCCACAGAGTTTACCTCCCGTATCCATTGCCAC
GTCCTATGTATCATTTAATTGCAAGATTTTTTGAGATGAATCCATTTGAGCCTTGGACAACAAGGGACAAAATTGATCGG
TTCCACACCACAGACACGAGATTCCCTAACCTTCCTGGATTGGAAGACTTGGGTGTCGTCCCAACCCCTGTAGAACTGAA
AGCCATTGAAGTCCTGCGGCGTCATCGTAAATATCTCTGGCTGGAAGCTGATCTCGATGAAGCAAAACCAGCTAGGACTG
TTAATAAC

Alignment

ORF - retro_acar_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.28 %
• Parental protein coverage: 98.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILHHDRQVHYSVIPHGKSGRSSVSGVVATVFGATGFLGRYVVNRLGRIGSQVVIPYRCDQYDLMYLRPMG
          .LHHDRQVHYSVIPHGKSGRSSVSGVVATVFGATGFLGRYVVNRLGRIGSQVVIPYRCDQYDLMYLRPMG
Retrocopy MLHHDRQVHYSVIPHGKSGRSSVSGVVATVFGATGFLGRYVVNRLGRIGSQVVIPYRCDQYDLMYLRPMG

Parental  DLGQLLFMEWDSHDKDSIRRALEYSNVVINLIGKEWETRNFKYEDVFVNIPRNIAQLSREAGVEKLIHIS
          DLGQLLFMEWDSHDKDSIRRALEYSNVVINLIGKEWETR.FKYEDVFVNIPRNIAQLSRE.GVEKLIHIS
Retrocopy DLGQLLFMEWDSHDKDSIRRALEYSNVVINLIGKEWETRSFKYEDVFVNIPRNIAQLSREVGVEKLIHIS

Parental  HLNADVKSPSKYLRNKAIGERVVREEFPDAIILKPSEMFGREDRFFNHYANMHWFGGVPLIAFGRKTVKQ
          HLNADVKSPSKYLRNKAIGERVVREEFPDAIILKPSEMFGREDRFFNHYANMHWFGGVPLIAFGRKTVKQ
Retrocopy HLNADVKSPSKYLRNKAIGERVVREEFPDAIILKPSEMFGREDRFFNHYANMHWFGGVPLIAFGRKTVKQ

Parental  PIYVSDVAKAIISAIKDPDAKGKTYTLTGPHRYLLYDLVQYLYAVLHRVYLPYPLPRPIYHLIARFFEMN
          PIYVSDVAKAIISAIKDPDAKGKTYTLTGPHRYLLYDLVQYLYAVLHRVYLPYPLPRP.YHLIARFFEMN
Retrocopy PIYVSDVAKAIISAIKDPDAKGKTYTLTGPHRYLLYDLVQYLYAVLHRVYLPYPLPRPMYHLIARFFEMN

Parental  PFEPWTTRDKIDRFHTTDMRFPNLPGLEDLGVVPTPVELKAIEVLRRHRKYRWLEADLDEAKPARTVNN
          PFEPWTTRDKIDRFHTTD.RFPNLPGLEDLGVVPTPVELKAIEVLRRHRKY.WLEADLDEAKPARTVNN
Retrocopy PFEPWTTRDKIDRFHTTDTRFPNLPGLEDLGVVPTPVELKAIEVLRRHRKYLWLEADLDEAKPARTVNN

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	5.74 RPM	25.08 RPM
SRP009831_brain	12.64 RPM	47.96 RPM
SRP009831_dewlap	12.02 RPM	56.87 RPM
SRP009831_embryo	20.01 RPM	36.60 RPM
SRP009831_heart	37.82 RPM	104.08 RPM
SRP009831_liver	6.30 RPM	31.90 RPM
SRP009831_lung	3.07 RPM	22.32 RPM
SRP009831_ovary	10.46 RPM	42.51 RPM
SRP009831_skeletal_muscle	12.35 RPM	64.14 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_16 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_16 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000009588	1 retrocopy	retro_acar_16 ,
Danio rerio	ENSDARG00000070723	1 retrocopy	retro_drer_1,
Homo sapiens	ENSG00000139180	1 retrocopy	retro_hsap_2585,
Gorilla gorilla	ENSGGOG00000006076	1 retrocopy	retro_ggor_1618,
Macaca mulatta	ENSMMUG00000020813	1 retrocopy	retro_mmul_648,
Monodelphis domestica	ENSMODG00000018283	1 retrocopy	retro_mdom_209,
Nomascus leucogenys	ENSNLEG00000003252	1 retrocopy	retro_nleu_1520,
Otolemur garnettii	ENSOGAG00000005225	1 retrocopy	retro_ogar_2244,
Pongo abelii	ENSPPYG00000004171	1 retrocopy	retro_pabe_1905,
Pan troglodytes	ENSPTRG00000004557	1 retrocopy	retro_ptro_1511,
Ictidomys tridecemlineatus	ENSSTOG00000006504	1 retrocopy	retro_itri_543,